


Survival [of the Foolish]

by ZedElla (Leviarty)



Series: Survival + Snippets [1]
Category: Stargate Atlantis
Genre: Ancient Technology, Excessive use of the Botany Department, Friends to Lovers, Independent Atlantis, M/M, Politics, Sentient Atlantis, Slow Build, Survival, sort of
Language: English
Status: Completed
Published: 2015-08-09
Updated: 2016-01-30
Packaged: 2018-04-13 17:50:09
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 8
Words: 21,221
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4531356
Author URL: https://archiveofourown.org/users/Leviarty/pseuds/ZedElla
Summary: <blockquote class="userstuff">
              <p>"We’re survivors, John. Thousands of years of evolution have told us that. But it’s going to be rough. Take care of your people."<br/>The screen went black.</p>
            </blockquote>





	1. Loss

**Author's Note:**

> Okay, so I've made some fairly massive edits to this (some 3000 words of edits...), so if you're coming back to reread this, you might find some changes. Overall the story is the same, a few scenes have been reordered and added to, and it's all still compliant to the rest of the series. The most notable change is that instead of one giant chapter, it can now be consumed in bite sized pieces.

Seven years after the expedition left Earth the first time, it happened.

It was sudden, but then, these kinds of things seldom came with much warning.

Atlantis dialed Earth on a Tuesday, and 0800 Earth Standard time (it was the middle of the night on New Lantea). They did so every week, like clockwork (though the longer days on Lantea meant that the time was a little different each week), and every week Earth was there to receive mission reports, status updates, supply lists, and to deliver directive changes. But on this particular day, Earth didn’t answer the call. It wasn’t an unheard of situation – sometimes the weekly report happened to coincide with an SG-team returning home, or an off-world emergency tied up the Earth ‘Gate for a few minutes.

As per protocol, Earth was dialed again 30 minutes later. But still, the ‘Gate would not connect. When the connection failed for the third time, Sheppard started to worry.

“Calm down, Rodney,” he said, though inside he felt equally antsy. It was unusual for the Earth ‘Gate to be down for so long. “I’m sure everything is fine.” He wasn’t sure, not at all, but as the leader of Atlantis, he couldn’t afford to let his own fear show.

 

Rodney set up a program to dial Earth every hour, on the hour, but on the third day, John made him shut it down. “We can’t afford to keep drawing energy from the ZPM,” he said. What he didn’t say was that it was futile to keep dialing, when the might not even be an Earth left to dial. Still, when the tower was quiet, he would have the technician on duty dial once in a while, just in case.

Rodney continued to panic, continued to theorize about all the things that could have taken the ‘Gate offline – sustained energy weapons, black holes, SGC self destruct. The theories got less pleasant the more time went by, but John understood his need to keep thinking. If he could uncover the problem, he could  _solve_ the problem. The possibility that it wasn’t solvable wasn’t something either of them was willing to think about.

“The Daedalus is scheduled to be back in Pegasus in 8 days,” Sheppard told him. They would know something. Assuming they were okay and made it back.

But keeping secrets was damn near impossible in Atlantis, and before long everyone was frantic, asking what could be done, hypothesizing about worst case scenarios.

For John, the fear was only superficial, little different than what Teyla and Ronon felt. Earth hadn’t been his home in years, hadn’t even been his home when it was the only place he knew. He feared for the friends he had made – Sam and Teal’c and Cam and a dozen or so people who bounced back and forth between Earth and Atlantis – feared for Rodney, who would be devastated if anything happened to his sister. Mostly, he feared what it would mean to be cut off from Earth once again, to not have constant communication and regular supply runs.

 

By the end of the first week, Dr. Robinson had started making the rounds, checking in on the mental well being of all the people of Atlantis. By day ten, she was sitting across from Sheppard. “How are you handling the present situation?” she asked. She didn’t carry a notepad, didn’t jot down thoughts and observations until later, in an attempt to seem more personable, less like a psychologist, but still he knew exactly what she was doing.

“What is this, a surprise session? Lure me with talk of the team, when really you just wanna talk about my feelings?”

She cracked a smile. “Not exactly. I do need to get an idea of your mental state though. You’re the leader of Atlantis, after all, I imagine that comes with a lot of stress, and now with what has happened…”

“We have no idea what happened.”

“Exactly. And I wonder how you’re handling it.”

Sheppard sighed and shook his head. “I’m fine. And before you say it, no, I’m not just being macho. I am okay. I had, sorry,  _have_ a few friends at the SGC. I’m concerned, of course. But I’m okay.” For the moment, he was trying to operate as though Earth was just fine, that the ‘Gate had gone offline or been damaged and they hadn’t had time to replace it yet. Atlantis would hear from them soon. “How are my people doing, in your professional opinion?”

“They’re worried,” she said. “Many of them have family and friends they now have no ability to communicate with. Some of them are handling it better than others, but they are all worried.”

Unfortunately Sheppard couldn’t do anything to alleviate their worry. He had no more answers than they did, no idea what had happened on Earth. And he wouldn’t lie to them, wouldn’t give them false hope.

 

“Robinson talk to you?” Rodney asked him over dinner. The meal tonight consisted of a purplish substance like mashed potatoes, some kind of maize, a red vegetable he didn’t have comparison for, and, if the supply logs were correct, the last of the real meat they had.

Sheppard nodded. “You too?”

“She thinks I’m bottling up my emotions and that my refusal to deal with reality is going to hamper my ability to do my job. I told her to stuff it.”

John almost chuckled. Instead he said “You’re sure you’re okay?”

“No, I’m not okay,” he snapped. “But it’s only been ten days. It’s too early to begin funeral processions without confirmation that something actually happened.”

What they both knew, but hadn’t said, was that Daedalus should have arrived in Atlantis that day, if they’d stuck to their schedule. Even running late, they should’ve sent some kind of subspace transmission…

 

On the nineteenth day, with still no word from Daedalus, they got the first message. It was the middle of the night, the control room was all but empty, and John was almost grateful for it.

“Do we have any off world teams?” Sheppard asked when the ‘Gate activated. He was certain that the answer was no, that all his people were on base, but through his exhaustion, he might have missed something.

“None, sir,” Banks confirmed. The event horizon formed, and the shield rose.

The gate was active for only a few seconds before shutting down again.

“We’ve received a compressed transmission,” Banks said.

“Decompress and send it to my office,” Sheppard instructed before walking back down the path to his office. Even years later, it’s hard not to think of it as Elizabeth’s. He was the third leader since she’d been gone, but still some of her knick-knacks lived there as a constant reminder of her, a reminder that his way is not always the right way, or the best way.

It was a few short  minutes before a video appeared on his terminal. “ _Atlantis, this is Colonel Sam Carter, Identification code 1-2-0-Alpha-0-Niner-8-8-Echo, coming from Earth Colony Helios_.”

“What the hell,” Sheppard mumbled to himself, but a smile had formed across his face the moment Sam had appeared. She looked rough, tired, but she was alive.

“ _I imagine you a little surprised to be hearing from me. To be honest, we’re still a little surprised on our side. Unfortunately, I don’t bring glad tidings.”_ She paused for a moment. _“There is no easy way to say this, so I’ll just come out with it: Earth is gone._ ”

Though it had been among the hypotheses, among the many possibilities they feared, nothing could’ve prepared him for those words, nor the feeling that came with them.

“ _Our sun exploded,_ ” she explained. She was fiddling with a chord in her hands, a sign of anxiety he’d never seen in her. “ _And before you jump to conclusions, no, it was not my fault._ ” She cracked a smile at that, but it was empty and mirthless.

Sheppard had read the missions reports, knew she once  _had_  blown up a sun; not to mention he’d been present when Rodney blew up the better part of a solar system. It wasn’t out of the realm of possibility that one of their own scientists would cause unfathomable destruction.

“ _By the time we realized what was going on, we only had about thirty hours to come up with a solution. We still don’t know exactly what caused it to happen. Dr. Lee and I and a dozen SGC scientists worked through all thirty hours, trying to find something… anything. In the end, we weren’t successful._

 _“During that time, evacuations were moving as quickly as humanly possible. Believe it or not, we have a contingency for this kind of thing. Anyone with a subcutaneous transmitter was beamed up, then back down to the SGC._ ” That made sense, John thought. It was a hell of a lot easier to deal with the people who already knew about space travel; then they could help facilitate the rest of the evacuations. “ _After that, small groups were beamed at random. It caused mass panic, of course, but there was no other way. There wasn’t time to explain what was happening, and we all… we all knew that not everyone would survive. Any kind of broadcast, telling people that some would make it and some wouldn’t; it would just make matters worse. As it was, there were riots. All they knew was that people were disappearing from the streets._ ”

She sniffled a little, and the feed went dark for a moment. When it came back, her eyes were red, but it didn’t look like much time had passed. “ _I’m sorry, John. We did what we could, evacuated as many as we could through the gate, then filled all our ships and got the hell out. We abandoned a lot of people. A fraction of a percent of Earth survived. Things haven’t exactly been easy since._

_“We’ve got three colonies out here, Helios, Hyperion, and Hemera. I’ve included the gate addresses in this transmission.”_

John silently questioned the wisdom in continuing to name everything after Greek tragedies.

 _“We’re… trying to settle in, but it’s been rough. We had bases built on all three worlds, but not enough to accommodate this many people, and our supplies are dwindling faster than we would like. We’ve got a few hundred thousand people trying to learn a way of life most of us have never considered, on top of a lot of morning. Tension is running high but… I don’t know._ ” She shrugged. “ _I think we’ll make it._ ”

The screen went dark, and she came back looking showered and refreshed, but still not the glowing beauty she usually was.

“ _Okay, on to the next order of business. I’ve spent the last several hours trying to figure out how to broach this, but I haven’t come up with anything good, so here goes. There is a delegation on its way to Atlantis now. At the time of my filming this, they were eight days out, by the time we get enough power routed into the gate to send this to you, they should be about halfway. Which means you’ve got about ten days to prepare. I don’t envy the position you’ll be put in. I don’t know exactly what they’ve got in mind, but the main topic is how to proceed as a society. I’ve included a document that details what we think might happen. I know you’re not a politician or a diplomat, but you’re gonna need to start acting like one. We have no doubt that they will try to take Atlantis from you. It’s not what we want, and know that you’ve got people on your side, but it might not be enough._

_“And finally, I’ve included a list of survivors. I can’t guarantee that it’s complete, because things are still a little messy around here, but it might help for some of your people to know their loved ones made it. Or give them some semblance of closure if they didn’t._

_“We’re survivors, John. Thousands of years of evolution have told us that. But it’s going to be rough. Take care of your people._

_“Helios out._ ”

The screen went black.


	2. Grief

He didn’t know how long he sat at his desk, debating what to do next, before finally having Banks call an emergency senior staff meeting. He didn’t know what he was going to say when they arrived, but he thought they might be the easiest and most logical place to start.

Only when he started to explain did he realize just how far from easy it was.

“They gave me, um, gave me a list, names of those who are confirmed to have survived. Rodney, your sister and niece are both okay, but Kaleb didn’t make it. Lorne, your mom and sister didn’t make it, but your nephews did.” Their names were the first he’d looked for, and he didn’t know what it meant that he didn’t know anything about the families of the rest of his senior staff. He knew Carson’s only family had been his mother, and she’d died over a year ago. But Zelenka and Teldy and Robinson… he’d heard them mention family over the years, but didn’t know a damn thing about them. "I'm sorry."

“Just a brother,” Teldy said when prompted. “Lt. Steven Teldy.” Sheppard found his name quickly, near the top of the list of SGC personnel who were confirmed survivors.

 “I have a very large family,” Zelenka said. “Perhaps it would be easier to just give me the list; I will search for myself.”

“Perhaps you should give us all the list,” Robinson suggested.

Teldy nodded in agreement. “Someone has to deliver the news, and you can’t do it on your own.”

Sheppard didn’t have the energy to argue. They were right, of course. Delivering the news to them had been hard enough… passing it along to the rest of his people felt like an impossible task.

“Teyla, Ronon, you don’t have to…” They were not from Earth, not bound by duty.

 

They couldn’t keep the secret long – not with a half dozen people in the control room when the call came through and the incredible speed at which rumors traveled the city.

On the twentieth day, he called the whole expedition into an assembly – with over three hundred, it could not be done in the gateroom, as it once could, and so they found a large meeting hall at the base of the tower, and called everyone in.

Sheppard hated this part more than anything, delivering the news of death to loved ones. This was the reverse of how it normally went, but telling them all at once made it that much worse. He was glad to have Lorne and Rodney standing beside him.

“As many of you are now aware, we received a transmission late last night. Unfortunately, that transmission did not come with good news.” He paused, took a deep breath. “Earth is gone. Only a small fraction of the population survived.”

A roar of voices broke out, drowning out anything he might have to say next. He brought his hand to his eyes, pinching the bridge of his nose. As a leader, he wasn’t supposed to show weakness, but this… was too much.

He heard Lorne shout something and the expedition fell silent again.

“I know you all have questions. I don’t have many answers. I wish I did. I wish I had more to say, because I’m sorry isn’t enough. All I have is this: a list of survivors. Colonel Lorne, Dr. McKay, and myself will spend the next couple of days calling each of you in to search for the names of your loved ones. It will take time, and I beg you to be patient.

“You’re the best and brightest Earth had to offer,” he said, and immediately regretted it, because the last thing anyone needed was to be reminded of Elizabeth, on top of everything else. He certainly didn’t want it, but times like these… the best he could do was channeling her. “The next few months might be harder than any of us can imagine, but we will get through it.”

 

“I would like to assist in notifying the staff,” Teyla said, approaching John after he dismissed the group.

He started to shake his head, decline the offer. He’d already said she didn’t need to. He’d paired them up to deliver the notifications: McKay and Teldy, Lorne and Zelenka, Robinson and Beckett. Because he didn’t want any of them to be alone in it, and upon a moment’s thought, he didn’t want to be alone either. “I’d appreciate that, thank you ,Teyla.”

“Your world was far bigger than mine ever dreamed to be. I cannot begin to imagine how that must feel. But I do know the affects of a great culling. No one should be alone in their mourning.”

 

It took longer than he expected. He found himself needing to take far too many breaks. For every person who got good news, two more got bad. And John had never been good at this, handling the grieving family. It was worse here, because the people grieving were his people, people he saw and worked with every day.

“You do not have to finish this today,” Teyla said. “You can rest, come back tomorrow.”

John shook his head. “It’s hardly fair to tell them that they’ll have to wait because I can’t handle it. I can deal.”

She pursed her lips, but nodded.

 

“Are you okay?” Rodney asked upon entering Sheppard’s room. He hadn’t knocked, but then, he rarely did.

John shook his head, his eyes still closed.

“Did you… lose someone?” Rodney asked. They didn’t talk about this often, family stuff. John knew Jeannie and Madison well, but anything else? They didn’t talk about it.

“No,” he said. “My parents were already dead. Haven’t talked to my brother in fifteen years. My ex-wife…” He shrugged. “It’s not like we were close. The only people I really care about are here. Mostly I just feel terrible that I don’t feel more terrible.”

“I’m just glad my sister and her kid are okay. God, I don’t even care that her husband didn’t make it. How horrible am I?”

“Asshole Lantean’s, party of two.” Only when he said it, did he recognize the truth behind it. Not the asshole part… But while the survivors should be banding together as Terran’s, he  realized he hadn’t been Terran in a long time. Atlantis was home, far more than Earth had been.

“Hey, you said it, the only people we care about are already here. Earth hasn’t been home in a long time. Thing is, well, those of us from the original expedition…”

“Yeah.” John understood. Everyone in Atlantis knew there was a possibility that they might die, might not make it back. The original expedition had already made their peace with never returning. It was years ago, things had changed, and no one expected that Earth wouldn’t be waiting for them, but Sheppard had seen the difference in their eyes. “I’m worried about the newer people. Maybe we should… I don’t know. I’ll talk to Dr. Robinson in the morning. It’s kind of her job, isn’t it?”

“I don’t think it’s in anyone’s job description to handle the grieving of an entire planet.”

“Yeah well, it is what it is.”

“I’ll get outa you’re hair,” Rodney said, rising from the couch.

John stopped him when he reached the door. “Thanks,” he said. “For helping out today.”

“Of course.”

 

 “Dr. Robinson approached me today,” Teyla said the following day.

“Really?” Rodney asked, surprised. “You’re not even from Earth.”

“I believe that’s why she wished to speak with me. She wanted to know how the Athosians, and other peoples in this galaxy, dealt with great loss. I believe she is… out of her depths.”

“We all are,” John said, sitting down at the conference table. “Did you two come up with any ideas?”

Teyla frowned. “Your people are very different from mine.” The Athosians were a small group, and even a great culling did not cost them so many. There was, however, no one in her village who did not know one another, and as such, the mourning that followed a culling was widespread.

She understood, of course, that Atlantis was not a representative example of what Earth was like. Here there were no kin groups, no children except Torren and another Athosian. That lack of familial bonds made for a very different grieving process.

“People should look out for one another,” she said. “There is little else I can suggest. On Athos, those who lost the most would not be left alone for many days, nor would they be required to attend to their usual duties.”

Rodney shook his head. “I understand not leaving people alone, but I won’t tell people they can’t work.”

“Rodney-” she started to argue. Surely he wouldn’t force people to continue their work at such a time.

“I don’t think he means what you think,” John said. “Many of our people, especially the ones here, prefer to work, than be left to their thoughts.”

Teyla nodded slowly. “And in ignoring your grief, you prolong it. I’m sure Dr. Robinson would agree that it is unhealthy to do so, and perhaps even dangerous to the other members of this expedition.”

“Maybe we could have a community grieving day,” Lorne said. “We already have mandated rest days to get people out of their labs for a few days. It wouldn’t be a terrible thing to do something similar.”

 

As expected, most of the expedition was not to fond of abandoning their work for a few days, but Sheppard demanded it of those who had lost all or most of their family back on Earth, and asked a few of those who didn’t to help them through it. Teyla and Robinson set them up in small groups around the central parts of the city, gave them candles, and talked to them in what could be described as only slightly condescending voices.

Sheppard sat in the control room in his civilian clothes – which looked not unlike his base uniform – and dialed Helios. It was several minutes before the gate technician was replaced by Sam Carter, looking exhausted, and a little grimy. She perked up a little at the sight of him.

“Hi Sam,” he said, and Rodney echoed the sentiment from somewhere behind him. “Did I wake you?”

She shook her head. “ _Been working. And damn it’s good to see you guys_.”

“You too. We feared the worst when we couldn’t make a connection.” Of course, the worst  _had_ happened, but there were survivors, Sam was among them. Everything would be okay. “Everything okay out there?”

“ _As okay as can be expected_ ,” she said. “ _None of the Alpha sites were really designed to handle this many people, so it’s been tough making space. After the initial chaos and panic wore off, things got a little easier. We’ve set up temporary living arrangements, but people are starting to get fussy. How are you all faring?”_

He knew they were doing a hell of a lot better than the colonies were. They had set living space, a steady stream of food, and a fairly stable command structure – he expected they had none of that. “Everyone has been notified of what has happened. We’re still in shock.”

“Robinson has us on a mandatory Day of Grievance,” Rodney said, sounding only slightly irked.

Sam nodded. “ _We had something similar a couple weeks back. I’m sorry it took so long to reach you. As it stands, were lucky to have had the power to dial you for those few micro seconds._ ” She looked offscreen somewhere, focused on what someone was saying, and nodded. “M _y guys are trying to get to work on installing our new iris, and they’re a little leery of doing it with an active wormhole. As far as your scheduled dial-ins… to be honest, we have much bigger fish to fry that reviewing everything you guys are up to. I expect to hear from you every week, but I don’t need mission reports and all that. Just to know that you’re all okay._ ”

“Sure thing. What about the other colonies? Are they going to freak out if I don’t check in with them.”

She shook her head. “ _It was agreed that all communication with Atlantis would go through Helios_.”

“Alright. See you next week?”

“ _Next week.”_

He terminated the connection.

“Can I go back to work now?” Rodney asked.

“No,” Sheppard replied.

“Come on, I didn’t even lose anyone. I’m perfectly happy and not going to break down in my lab and cause an explosion. Scouts honor.”

“You were never a boyscout. Come on, we can play video games in the screening room, or something.”

“Can’t you just spar with Ronon for entertainment? Some of us, namely me, have actual work to do.”

“Ronon is off world talking with some of our trading partners.”

Rodney looked around for a moment. “Huh. I hadn’t even noticed he was gone.”

“Come on, Rodney,” he said, taking his sleeve and tugging him toward the stairs.


	3. Delegation

**Notes for the Chapter:**

> Assume that at some point Lorne was promoted from Major to Lt. Colonel. He deserves it.

Sheppard spent the next several days, along with McKay and Teyla and Lorne, reading through the numerous files Sam had sent them, each one weighing them down further.

“We’re gonna lose the city, aren’t we?” Rodney said, setting his tablet down. “They’re gonna come in and take over and ruin everything.”

“Not if I have any say,” John said. In truth, he had no idea. Things weren’t looking in their favor, but surely someone had pointed out the dangers to the  _delegation_ , whoever they were.

 

“A ship just dropped out of hyperspace,” Sgt. Wagner announced. “Reading Daedalus IFF.”

“They’re early,” Sheppard said with a hint of dread.

“ _Atlantis, this is Caldwell, permission to beam down the delegation.”_

Sheppard pressed the tile to respond. “It’s good to hear from you Colonel. Permission granted.”

He straightened his back, crossed his hands behind his back, and reminded himself to be on best behavior. Getting into a brawl would only worsen matters.

Six people beamed down, five of them wholly unfamiliar, and the sixth –

“General O’Neill.”

“Colonel Sheppard. Good to see you.”

“You too, sir.”

“May I introduce Sun Rou, Raya Mednikova, Kiran Sidhu, Koyanagi Yosha, and Martin McLaughlin. The New World Leaders. This is Colonel John Sheppard.”

“We have much to discuss,” Sun said. “We should begin. I assume you have a meeting room of some kind?”

“Of course, this way.”

Sheppard lead them across the way to the conference room, his anxiety rising with each step.

He had first thought that O’Neill was just the escort, there to keep the delegation happy or in check or out of Caldwell’s way, but in moments he realized that was not the case. He was the North American representative. Suddenly, Sam’s words about being on their side made sense. He had at least one friend at the table, and he couldn’t be more grateful for it.

 

“Absolutely not,” Sheppard said, for at least the fourth time. They had been arguing for hours, if arguing could be defined as a table full of people not listening to reason. They kept making the same points, and Sheppard kept shooting them down. If O’Neill’s expression was anything to go by, he’d been having the same discussions with them for much of the trip to Pegasus.

“You have said yourself that this city can house a couple million people. Our numbers are well below that. 750 thousand, no more. By your estimation, there is more than ample room for every single survivor of Earth.”

“Mr. Koyanagi, I’m not denying that there is space. I’m denying the wisdom in what you’re suggesting. Pegasus is a dangerous place. We are winning the war with the Wraith, but there have been mass casualties. In the seven years we’ve been here, over 800 people have been stationed here. Over a third of them have died.”

“Then we isolate ourselves,” Sun said. “My understanding is that use of the Stargate has caused many more problems than it has solved. So we stop using it. Confine ourselves to the city, halt all exploration of the galaxy.”

Sheppard laughed at that, and he saw O’Neill crack a smile. They both knew what the rest of the delegation refused to see.

“It’s not an option. If we did, in fact, live in the magical fantasy world where the Wraith did not exist, then we would still need the Gate for food, at the very least. Our botanists can only grow so much in the labs. Even when we had monthly supply drops from Earth, we had to supplement by trading with agricultural societies. The fact is, the Wraith _are_ a serious threat, andthey aren’t going to stop hunting us, or killing everyone else in the galaxy. Isolating ourselves is not an option.”

“More to the point,” O’Neill said. “The Wraith aren’t the only danger out here. Atlantis herself is.”

“What do you mean?”

“Dozens of people have died in this city,” Sheppard told them. “We are dealing with Ancient technology we hardly understand. We’re learning a lot, but there is a definite risk involved. All of my people know that, agreed to take that risk when they came here. But there is nothing to stop some civilian from wandering into a lab and getting themselves and others killed because they have no idea what they’re messing with. My people are geniuses and it happens to us on a regular basis. I won’t allow anyone else into this city; it will only put all of us in danger.”

“You may not have a choice,” Sidhu said.

“I do not understand why you cannot simply block dangerous areas.”

Sheppard jumped to his feet and walked out. “Follow me,” he called over his shoulder. He passed behind the control room and called for McKay and Lorne to join them. He didn’t remember the transporter being large enough to accommodate nine people comfortably, but somehow it was. “Ms. Mednikova, please pick a tower,” he said, motioning to the map of the city.

She hesitantly pointed to the northwest sector, which Sheppard tapped, then adjusted the coordinates.

“Oh, I don’t know if that’s-” Rodney started to say.

“Nope, I think it’s an excellent idea,” Sheppard said. If he sounded a little manic, only those who knew him recognized it. “New World Leaders, this is Dr. McKay, our Chief Scientist, and Lt. Colonel Lorne, military commander. Doctor, Colonel, meet _the Delegation_.”

The teleporter stopped and the doors opened.

The floors were wet, and Koyanagi nearly slipped when he stepped out.

“As you can see, this area was, until recently, flooded. This is a problem we’ve been having since we first arrived seven years ago. Just when we get rid of the water in one section, another area floods. It hasn’t exactly been a top priority, since the work is futile. This particular area is residential, as are many of the lower levels. It would take months, potentially years to secure enough space to accommodate all the survivors and ensure that many of them aren’t in danger of drowning at any given time.”

He led them up a couple flights of stairs. “The residential areas are somewhat mixed with the labs. We recently started exploring this area because our scientists found mention of, what was it, Dr. McKay?”

“Alternative transportation methods,” Rodney supplied. “But I strongly caution against going in there.”

“Yes, you mentioned that.” He turned his attention back to the delegation. “A pair of scientists, some of the smartest we have, came out here to do research.” He positioned them so they could all see clearly into the room, but didn’t allow them in. “You see the burn mark over there? That’s where Dr. Kuwagi died twenty-two days ago.”

He led them down the hall back into the transporter, and tapped a different area of the city. “A few months back we had a teleporter malfunction. It has since been fixed, but not before Lt. Howard ended up out here instead of his quarters. He walked into this lab by mistake, and had to be put on a ventilator and returned to Earth. Sending the wounded back home isn’t much of an option anymore.”

 

“They’re not taking him seriously,” Lorne said.

“Which is incredible because he’s kind of terrifying. I haven’t seen him like this since… well, I’m not sure if I’ve ever seen him like this. We were separated during Kolya’s invasion, but I always imagine it was a little like this.”

Lorne shook his head. “It doesn’t matter. We’re going to lose the city, and thousands of people will die.”

“Billions already have. If only there was some way to…” Rodney stopped talking, and Lorne could almost see the gears turning.

“Some way to what, Doc?”

“Come with me, Colonel.”

 

“Perhaps we should take a recess,” O’Neill said. “We could all use a little breather, maybe some dinner and rest.”

“Agreed,” McLaughlin said. “We will reconvene in the morning.”

The representatives filed out of the conference room, where Sheppard could see Lorne and a security detail were waiting to escort them.

“I’m guessing you already went over all of this with them,” Sheppard said, when it was only him and O’Neill left.

“Yep. In one ear and out the other. Show and tell was a nice bonus though.”

“I appreciate you backing me up, Sir.”

“Hey, I like Atlantis as much as the next guy. But it’s no place for a recently crippled society. It just a matter of getting them to see that. I do have some good news for you –and personnel transfers for you to approve.” O’Neill slid a tablet across the table to him.

Personnel transfers? For a moment, Sheppard questioned whether the General was really on their side at all, but one look at the transfer list answered his question. “All of them are aboard the Daedalus?”

O’Neill nodded. “Caldwell’s waiting for your okay. Look, shit might hit the fan, but for the moment we’re going to act as though Atlantis is still yours to command. Sidhu and I have been talking, come up with an idea to keep it that way. If you’re in agreement, then we only have to talk one other leader into it, and 4-3 vote will rule. We’ll have to get them off the idea of Atlantis first, of course, but I think once they realize it’s not a viable option...”

“What’s your idea?”

 

“I think we should hold off on these transfers,” Rodney said, looking them over.

“Really? Why’s that?”

“Look, I’m all for reuniting family groups, or whatever O’Neill said, but I think we should be cautious. Atlantis isn’t exactly suitable for children.”

“There are children on Atlantis.”

“Yeah, two of them, and they have gotten into more trouble than any of us would like. I’m not letting Madison or any of the other dozen kids come down here until I’ve had a chance to set up some safe guards.”

“You’re up to something,” Sheppard said, catching McKay’s eye.

“What? No I’m not.”

“You are. I have no idea what, but I know that look.”

Rodney eyed him defiantly. “I assure you, Colonel, I am doing nothing that you should be concerned about. I know the  _New World Leaders_  don’t understand our public safety concerns, but you certainly should. Give me forty-eight hours to get new security measures in place. Forty-eight hours or until the delegation leaves, whichever comes first.”

Sheppard narrowed his eyes as Rodney wandered away. He was definitely up to something, and it was unusual that he be so secretive about it, especially with him.

“Keep an eye on Rodney,” he said to Lorne, before returning to the conference room.

 

“Where is Mr. Koyanagi,” McLaughlin asked the following morning.

Sheppard tapped his earpiece. “Control room, can you get me the whereabouts of Koyanagi Yosha?”

“ _Just a moment, sir_.” There was a long pause. “ _I looks like he and his security detail are near the South Pier. Shall I radio them?_ ”

“Yes, sergeant.”

A moment later the comms were flooded with screams. He pulled the earpiece off quickly to protect his eardum, and knew the rest of the delegation could hear the screams.

“Sergeant, what the hell was that?” he asked.

“ _Working on it, sir_.”

An alarm blared loudly, and the conference room doors shut tightly. McLaughlin jumped to his feet and pushed on one to no avail.

“Don’t bother,” Sheppard said. “Citywide lockdown, those doors won’t budge.” He could think of no worse place to be trapped than with this bunch of arrogant diplomats. “Rodney, what’s going on?” he asked politely over the comms.

“ _I’m working on it_ ,” McKay shouted back.

“They’re working on it,” he informed the delegation. “In the meantime, we should return to our talks.”

“What is happening?” Sun asked.

“The city locks itself down in the event that a contagion is detected.”

“Contagion?!”

“It’s under control. The lockdown is to prevent the contagion from spreading. We’re safe in here, while my scientists work out what happened and disseminate a counteragent if necessary.”

“This has happened before?” Sidhu asked.

“Yes. I have the utmost faith in my peoples’ ability to solve this problem. Which brings me back to my previous point: I do not have that faith in the rest of the human race.”

“Your people have earned that faith, I’m sure, but you will not even give others the opportunity to do the same?”

“No. Not with hundreds of thousands of lives on the line. You asked why I can’t secure the dangerous parts of the city, or shut down the labs that were running dangerous experiments: the answer is that we don’t know enough. We’ve been here for years, but we’ve only explored a fraction of this city. For good reason. The labs and residential areas are not segregated. There is no way to open access to one without opening the other. We enter one lab at a time, and it can take days, sometimes weeks to figure out what its purpose is, how to shut it off permanently, and make sure it’s not going to kill us. Most of these things don’t have an on-off switch. They have to be carefully dealt with. Otherwise  _this_  happens.”

“What exactly is happening?” Sidhu asked.

“McKay, update,” Sheppard requested into his earpiece.

“ _Near as I can tell, one of your New World Shitheads found himself in a medical research lab, and was exposed to a virus. The city sensors picked up on it when they tried to return to the main tower, city defenses kicked in. Carson is working on reverse engineering a cure based on the information in the Ancient database. Give me two hours._ ”

Sheppard relayed the necessary information to the delegation.

“What of Koyanagi?” Sun asked.

“He’s being cared for.”

“What does that mean? What happened to him?”

“We’re still trying to figure that out.”

“I think the situation speaks more than Colonel Sheppard’s words can,” Sidhu said. “It is as O’Neill has been trying to tell us the last many days. Atlantis is not safe for our people. Let them stay, if they wish to continue to endanger themselves, but I will not be party to the continued deaths of my people.”

“Thank you, Ms. Sidhu,” Sheppard said.

“I think it’s all quite convenient,” McLaughlin said. “Too convenient. You don’t want to share your precious city, so you concoct some scheme to show us how dangerous it supposedly is. I doubt if there even is a lockdown.”

“Let me tell you something Mr. McLaughlin: I would not volunteer to be locked in a room with any one of you for several hours, let alone all of you. Nor do I make false claims of very serious situations. We lose lives here, more often than I like. We have hundreds of safeguards in place to ensure that number stays as low as possible. If you force several hundred thousand refugees in here, there will be no way of maintaining those safeguards, and more people will die.”

“I have a proposal,” Sidhu said. “It has been brought to the table in the past, but you all were so determined to have this great city that you could not see logic. Perhaps with what has transpired…”

 

“McKay, for the love of god, end this lockdown. Or at least give me some good news.”

“ _Sorry, sir, Dr. McKay is off radio_ ,” Banks informed him.

“What? Where is he?”

“ _Colonel Lorne has just gone to find him_.”

“We have agreed to your terms, and still you will not let us leave, why?” Sun asked.

“You people must be the biggest idiots,” Sheppard said. “We’re not holding you hostage,  _the city is under lockdown_. I’m sure our scientists are working as quickly as they can, but I am no happier to be here than you are.”

 

They sat in near silence for another forty-five minutes before the doors finally shifted open.

“Finally,” Laughlin exclaimed, jumping to his feet.

“Sir,” a Marine said, making eye contact with Colonel Sheppard.

“What is it, Sgt. Caffrey?”

“You’re needed in the infirmary. It’s Dr. McKay. He’s been injured.” Sheppard didn’t need to be told twice, and took off running down the steps to the infirmary.

“I would like to see Mr. Koyanagi,” Mednikova said.

“I’ll show you the way,” O’Neill said, and led the delegation down to the infirmary.

They first see Sheppard standing the bed of Dr. McKay. His face and arms were covered in burns. Sheppard’s hand was on the bed, near McKay’s, though he carefully did not touch, for fear of making the pain worse.

Two beds over, a Marine was lying in a similar state, though his more severe burns were wrapped in bandages.

“I doubt whether either of them is going to make it,” Carson said, his voice sounding much stronger than his face appeared. “Mr. Koyanagi has an upper respiratory infection, but it’s not so contagious as the city thought. I’ve got him on antibiotics. He can return to work as soon as he wakes up.”

“Is he in pain?” Sheppard asked.

“Koyanagi? Not severely, no.”

“No. Rodney. Is he in pain?”

“For the moment, no. I have him on powerful sedatives. He’s not feeling much of anything right now.”

Sheppard nodded.

“I think I should like to return to Hyperion now,” Sun said.

“I as well,” Mednikova said.

“I’ll wake Mr. Koyanagi, he can return with you.” He went to the medicine cabinet, then injected Koyanagi with something he found there. Within moments, the man was awake, but confused.

“What happened?” he asked, ending with a loud cough.

“We will fill you in later,” Sidhu said. “For now we must take leave.”

“But-”

“The decision is made, it is final,” Sun said.

“Colonel Lorne, perhaps you could escort our friends to the Gate?” Carson suggested.

“Sure thing, Doc,” Lorne said. He sent a tentative look at Sheppard before leading the delegation away.

“Good job,” O’Neill said, patting Sheppard on the shoulder.

“This isn’t some ploy, General,” Sheppard said.

“Of course not. Listen, Sheppard, you’ve got your independence now, but I think we’d all like to hear from you now and again, especially in the coming months. Still a lot of things to work out.”

“Yes, sir.”

“I’m not your superior anymore, call me Jack.” And then Jack was gone.

“Aye, what’s he on about?” Carson asked.

Sheppard shook his head.

A few moments passed before Lorne’s voice came over the comms. “ _The delegation is away._ ”

“About time,” Carson said, preparing a set of injections.

“What are you doing?” he asked as Carson administered the drug to both Rodney and Sgt. Seaver. Within seconds Rodney’s eyes opened.

“They gone?” he asked.

“Yes, Rodney,” Carson said, while Sheppard watched them with a look of shock and confusion.

“Thank god,” he said, then began picking at the oozing burnt flesh around his left eye.

“Rodney, what are you-” Sheppard started, feeling a little queasy. He watched as the burn peeled away, leaving smooth, clean skin. “It was a ploy. You bastard, I thought you were  _dying_.”

“Oh, come on, you knew I was up to something.”

“Yes, the lockdown I figured was your doing.”

“Exactly. I had to do something to convince even you, just so they would know it was real.”

“But it wasn’t real.”

“Of course not. But they don’t know that.”

“Koyanagi?”

“Minor respiratory infection. We may have led him into a lab we cleared a few weeks ago, made it look like an accident.”

“Think they bought it?” Lorne asked upon his return.

“You were in on this?” Sheppard asked. Lorne shrugged, but his smirk told all.

“Someone had to make sure I didn’t get completely out of line,” Rodney said. “And I couldn’t bring you in, so he’s the next best thing.”

“I’m honored,” Lorne said. “Now, someone mentioned new personnel?”

Sheppard smiled as it clicked into place. He hopped to his feet, tapped his earpiece, and began walking back to the gateroom, with Rodney and Lorne at his heels. “Dr. Kusanagi, Dr. Lindsay, Major Cadman, Major Teldy, Sgt. Mehra, Dr. Moore, Dr. Nichols, please report to the gateroom.” When he arrived in the control room he stood next to Banks and had her call up the Daedalus. “Colonel Caldwell, sorry for the delay, but we’ll be happy to take our people now.”

“Give us just a couple minutes, Sheppard,” Caldwell replied.

“What’s going on?” Cadman asked as she and several other arrived.

A few moments passed before the Asgard beams appeared, leaving behind almost two dozen people.

“Uncle Evan,” two boys shouted in unison, running into the open arms of Lorne.

“Tess,” Cadman said, bringing her sister into a tight hug. They were nearly identical, Sheppard noticed.

He watched as the few members of his team were allowed to reunite with their brothers, sisters, nieces, and nephews. After all the bad they’d been through, at least he got to witness this.

“Welcome to Atlantis, baby girl,” he heard Jeannie say to Madison as they walked up the steps, hand in hand.

John and Rodney walked to meet them halfway. Rodney hugged his sister, while John dropped down to Madison’s height.

“Hi, Uncle John,” she said with a smile, placing a kiss on his forehead. She did the same to Rodney when he joined them on the floor.

“Listen kiddo,” John said, prying his hands away from her. “I’m gonna leave you in the very capable hands of Uncle Meredith, while I go talk to Colonel Caldwell. I’ll be back in just a couple minutes, kay?”

“Mmkay,” she said, moving to sit next to Rodney. John smiled as she rested her head against Rodney’s shoulder.

Caldwell had come down in the second beam, accompanied only by a couple dozen crates.

“Colonel.”

“Colonel, it’s good to see you.”

“You scared off the World Leaders much faster than I expected.”

“You can thank McKay for that. He can be very convincing.”

“So I’ve learned. I was hoping you’d let us set down for a few days, get some repairs done. We’re space-worthy, but not much else.”

“Of course. East Pier is all yours.”

Caldwell called up to his ship and instructed Marks to land. “Care to fill me in on what went down?” Caldwell then asked.

“How much did O’Neill tell you?”

“Told me about his plan to have four distinct societies, to increase the chances that at least some would survive. Also said he didn’t think he’d be able to convince the delegation.”

“Well, we succeeded. Things are going to start changing around here, Colonel. I’d like for you to be a part of it, if you’re willing.”

“Is that really up to me?” Caldwell asked.

“That was part of the agreement. All the ship captains have their say on where their citizenship will be. Of course, if any of your people wish to be reassigned to the Milky Way, they should be allowed to do so.”

“How much time?”

“There is a two month transition window. During that time there will be a lot of shuffling around, I’m sure. Due to the unique dangers of Atlantis, transfers in must be approved, but anyone who wants out is free to go. I’ll be making the announcement tomorrow.”

“I’ll think on it, talk to my crew, let you know when I decide.”

“Take your time.”

 

 “We’re going to have to figure something out for the living situation,” John said, sitting down with Rodney and the Millers. “None of the quarters in the main tower are meant for families.”

“I cleared a section of Tower Two,” Rodney said, showing him his tablet. “Three floors of residential rooms. All access to the nearby labs has been blocked.”

“Any way to override those blocks?”

“Only if you and I are both present. Those labs have all been explored, catalogued, and shut down. The risk is minimal.”

“When did you have time to do this?”

“What did you think I meant when I said I needed time to set up safeguards?” Rodney asked.

“I thought you were buying time to enact your hair-brained scheme. Which, hey, we need to talk about you not pulling something like that again.”

“What did he do?” Jeannie asked.

“Faked a contagion lockdown and his death.”

“Mer-e-dith,” she said, enunciating each syllable of his name as she smacked him lightly.

“I didn’t fake my death. I faked being near death.”

“Which you must now promise to not do again.”

“Fine, I won’t do it again if you promise not to fly another suicide raid.”

Sheppard scrounged his nose. “Fine.”

“Great. How ‘bout we get these people out of the gateroom and moved into their new quarters.”


	4. Building

He made the announcement the next morning, kept it short and to the point, despite the fact that a lot of information needed to be conveyed. Atlantis was now an independent state, as were the three other colonies of Earth. Atlantis had been functional for years, even before the monthly supply trips. Things would be tough without Earth to back them up, but they had done it before, they would find a way to do it again. Things would have to change in the meantime.

 

“We have military from four different countries,” Sheppard said to Lorne over lunch. “And civilians from a dozen more. We’ve mostly followed US military rules and regulations, but I think it’s time to change that. It’s functional, but not practical.”

“I agree,” Lorne said. “Should I call a meeting with the non-American military personnel? I can work with them to write a new code to suits us all.”

“Sounds good. Take your time on it. And include Ronon.”

“Of course.”

“I also want to talk about the position of second in command.”

“Colonel Caldwell?”

Sheppard shook his head. “If he chooses to stay, he’s welcome to hang around Atlantis, and he will have a seat on the senior staff, but his place is on his ship. Now that I don’t have the IOA breathing down my neck, I’d like to have Teyla as my official second.” He knew she was a good leader, and didn’t want anyone else in charge of Atlantis if something should happen to him. On paper, of course, Lorne and McKay had been the only options. “But I need to know you’ll follow her.”

“Yes sir. I have more respect for her than anyone I’ve served under. She knows Pegasus better than any of us.”

“Damn right she does.”

“What about the kids?” Lorne asked, moving on to their next discussion point. “There’s a fair few of them now, and even with McKay’s safeguards, I’m concerned they might get themselves in trouble.”

“Zelenka is working on it. I’m hoping for some kind of tracking device that will alert us when they’re beyond certain areas, but we’ll see what he comes up with. The food situation?”

“We’re good for now, but I’ve arranged for three teams to scout for food sources. Teyla’s made a list of potential trading partners, and requested Teldy’s team to accompany her. My team will take Parrish to look around a few uninhabited planets, and Stackhouse is taking Dr. Brown. If we can gather enough angiosperm, and find ourselves a sizeable greenhouse to propagate them in, theoretically we can sustain ourselves indefinitely.”

“Please stop hanging out with the botanists,” Sheppard said, chuckling.

Lorne shrugged.

“Okay, I’m approving those missions. What’s next on your list?”

Lorne frowned. “Well, I’m not sure how you’re going to feel about this but… I think we need people to start having babies.”

“Excuse me?”

“I’m not saying we should pair people off and demand it,” Lorne assured him. “But we should certainly encourage it.”

 

“I don’t think I’ve ever seen you like this,” Jeannie said, toweling her hair dry as she walked out of her bathroom.

“Like what?” Rodney asked. He was sitting on the floor, playing board games with Madison.

“So good with Mads.”

“Hey, I’ve always liked her. Right kiddo?”

She looked up at him, her face drawn in strange manner. She shook her head, then added a checker to the board.

“Fine, we all know I’m terrible with children. Maybe I’m just glad you’re both okay.” His ears turned pink.

“It’s okay to be sappy, Mer,” she said, placing a kiss on the top of his head. “We’re glad you’re okay, too.”

She sat on her bed, running a brush through her hair, as she watched them play. “Hey, Mer?”

“Yeah?”

“You thought about having kids?”

“God no,” he said after a half second thought.

“Not even when you were with Jennifer? Or Katie?”

He shook his head. It had never crossed his mind.

“Maybe you should think about it.”

“And who exactly am I having these hypothetical children with? I don’t see volunteers lining up.”

“Whoever you want, I guess. But Atlantis isn’t very well populated. If this branch of Terran people is going to survive… people have to start making babies.”

“Other people. Not me.”

She laughed. “I don’t think you’d be a terrible father.”

“I have never been so honored,” he deadpanned. What point was she trying to make?

“What about you and John?” she asked after a while.

“What about him?”

“Well, are you and him…  _you know_?”

“What? No. Of course not. God, where did you even get that idea?” His ears flushed.

“Well you clearly like him. And he likes you. So I figured…”

“You’re clearly insane.”

“Maybe. Maybe not.”

“What are you suggesting, anyway? Because if you’re thinking we could get together and have a few kids, if that were even in the realm of sanity, I should point out that we would be missing a crucial ingredient.”

“Well, no, of course you wouldn’t be able to procreate without some assistance. I just thought. I don’t know.”

“Yes, you don’t know, and you should stop that line of thinking immediately.”

The door pinged. “Come in,” Jeannie said. “Hey, John, we were just talking about you.” Rodney’s ears turned pink again.

“Oh?”

“What do you need?” she asked.

“Your brother.”

“What it is?” Rodney asked from the floor.

“If I were looking for a greenhouse, where might I find one?”

Rodney thought about it for a moment. “Uhh… Tower three? I think it retained structural damage, we never got around to fixing it. Though, now I can see why it should be a priority. I’ll move it to the top of the list.”

“Thanks, Rodney,” he said with a smile, then turned to leave.

“Hey, John,” Jeannie called. “We were about to head to lunch. Would you care to join us?”

Sheppard shook his head. “I just came from there. Maybe I’ll catch dinner with you,”

Rodney waited until Sheppard left and the door closed before he said to Jeannie, “I hate you.”

“Come on, Rodney, isn’t it time you settled down?”

“I tried that. Twice, actually. You may have noticed that didn’t work out.”

“Maybe you should ask yourself  _why_ it didn’t work out. Because we both know the answer.”

Rodney groaned, staring up at the ceiling in exasperation.

“Rodney and John, sitting in a tree, k-i-s-s-i-n-g,” Jeannie sang as she moved around the room.

“Shouldn’t you be, I don’t know, moping around instead of harassing me?” The moment the words were out of his mouth he knew they were wrong. He sat up to apologize, catching the broken look on her face for only a moment before it turned to anger.

“And there’s the Rodney McKay we all know and love, rearing his ugly head.” And she  _never_  called him Rodney; she was pissed. He knew he deserved it.

“Jeannie, I’m sorry, I didn’t mean-”

“God, do you even think before you speak? It’s a damn miracle anyone can stand to be around you.”

He got up from the floor and wrapped his arms tightly around her. “I’m sorry, Jeannie. I wasn’t thinking. I’m sorry.”

She struggled for only a moment before accepting his embrace, burying her face in his shoulder. “You’re so mean,” she said, her voice muffled.

“I know. I’m sorry.”

 

 “Pegasus is a big place,” Caldwell said. “You can only explore the planets that have stargates.”

“But you have a very impressive ship.”

Caldwell laughed. “I never expected you to suck up, Sheppard.”

“Hey, if the answer is no, I’ll accept it and send you on your merry way. But until I have that answer, I will do whatever I have to do to ensure our survival. You’re right, our options are limited, we can only go where there are stargates. I would love to have your continued support when shit hits the fan.”

“Say I do agree to stay. What happens when my people want to take shore leave? Will they be allowed in Atlantis?”

“Of course. They will be expected to follow the same procedures as anyone else here. We’re still working out the details, but seeing that we are, _were_  an international team, new military and civilian codes are being designed as we speak. I should remind you that this is, first and foremost, a civilian base. The military is here for support only. Which means you will have limited power when you’re here. I’ll give you a seat on my senior staff, of course, but that is all; the final decision on all matters concerning this base, rests with me.”

“You make a compelling argument, Sheppard.”

“I spent the last three days dealing with the New World Leaders, despite the fact that we came to an agreement days ago. Before that, I spent nearly three years with the IOA on my ass. I  _live_  for the days when my most compelling arguments are with McKay on whether his latest experiment is worth the risk to public safety.”

Caldwell laughed again. “Tell you what, I’ve got to head back to the Milky Way colonies, pick up the remaining transfers. I’ll see what they’ve got going out there, then give you my answer when I return.”

“Sounds fair.”

“Is it still fair if I ask that Major Marks remain here to assist in the creation of your new codes?”

Sheppard smiled. “I welcome it.” The new codes were going to be a painful process, having one more person to help could complicate things, but it would also ensure that the codes were fair to everyone.

 

“Am I done with the political bull yet?” Sheppard asked, flinging himself onto Rodney’s bed. He had thought that the delegation leaving Atlantis meant the end of it, but every time he dialed one of the colonies to talk to Sam or O’Neill or just get a general update, he instead found himself fielding pointless questions from the rest of the New World Leaders.

Rodney stopped his furious typing for a moment. “You’re the leader of Atlantis,” he said, looking over his laptop. “I doubt you will ever be done with it. On the plus side, it’ll all be in house from here on out, no IOA looking over your shoulder.”

“You’re right. I could declare martial law, and no one could stop me.”

“You’re mad with power,” Rodney deadpanned. “So what did Caldwell say?”

“He’s gonna give me a definite answer in 39 days. Pretty sure he’s gonna say yes though. He just wants to make sure one of the other colonies doesn’t have a better offer.”

“If he thinks any of those blowhards are going to give him near complete autonomy, he’s as crazy as you are.”

“Excuse me, but I did not _fake an emergency_ and pretend to get myself killed just a few days ago.”

“Purely in the interest of self preservation. I’m not insane.”

“You’re a little insane, McKay,” John said, holding his thumb and index finger an inch apart.

“Aren’t we all?”

John smiled, letting his head fall back to the pillow.

“Get your shoes off my bed,” McKay said offhandedly. John toed the boots off, kicking them over the edge. “Don’t you have better things to do than hang around my room?”

Sheppard shrugged. “Not at the moment, actually. Hey, what’s this?” he asked, picking something up off his nightstand. It was a model of a puddlejumper, not much larger than a brick. It was in perfect scale, and incredibly detailed – down to the markings etched into the sides, and the interior seating and controls.

“Oh, that. I found it in a lab a few weeks ago. I’ve been meaning to give it to you.”

“Really?”

“I mean, I’m pretty sure it’s a children’s toy, but it seemed like something you’d like.”

“Thank you, Rodney,” he said, smiling. He was pretty sure he imagined the pink in Rodney’s ears. He turned his attention back to the mini jumper, and wondered briefly if it could fly. It took only that thought for the jumper to lift out of his hands, hovering just a little. He grinned, mentally guiding it toward Rodney.

“Huh?” he said, jumping a little in surprise as the jumper nudged him. “Oh. That’s actually pretty cool.” The drive pods slid out, followed by the drone compartments. “Please don’t shoot me. I’m pretty sure even tiny drones hurt.”

“I’m not going to shoot you, Rodney. I just wanted to see how detailed it is.”

“Incredibly so, it seems.”

“Well, the Ancients never did anything  _small_.” It could be argued that it was their grandeur that led to their downfall.

 

On the forty-third day, good news came around.

“You seem tense,” Ronon said as Sheppard hit through ground for the third time.

“I’m always tense. That’s why we do this.”

“More than usual, I mean.”

Sheppard rose to his feet again, careful to keep his eyes on Ronon the whole time. He raised his arms to cover his face, preparing to take another hit. “Too much of this political bullshit.”

“I thought things had calmed down since the delegation left.”

It had been many weeks, and though their absence was a load off his back, it didn’t take everything. “Yeah, everything with them is pretty much set, but I’ll be ecstatic if I never have to negotiate another trade agreement in my life.”

“I thought Teyla handled most of the trades.” He jabbed Sheppard in the ribs.

“Ow. Not with the Genii.” They were too difficult, had too much bad blood. It could be no one but John, as much as he abhorred it.

“ _Colonel Sheppard,_ ” a voice called over the speakers of Atlantis.

Ronon halted mid-kick as Sheppard’s attention shifted. “Go ahead,” Sheppard said.

“ _Colonel Lorne has been trying to reach you over comms. Non-emergency._ ”

“Thank you,” John said, grabbing his earpiece out of his abandoned jacket. “Sheppard to Lorne.”

“ _Hope I’m not interrupting anything, but I thought you might like to see something,_ ” Lorne said.

“What kind of something?” Sheppard asked. He really didn’t have the energy to deal with more flooded compartments, or weird science experiments, or any other broken Ancient equipment. Nonetheless, he put his discarded gear back on and headed for the door with a towel around his neck.

“ _It’s good, sir. But I’d rather not ruin the surprise._ ”

“You know I hate surprises.”

“ _You’ll like this one._ ”

Sheppard was a little doubtful of that, because surprises in Atlantis were usually attached to like-or-death situations, but Lorne seemed sure, and he didn’t often mislead.

And this time was no different, because when he arrived at the location as instructed, Lorne was standing outside the transporter waiting for him, all but bouncing on the balls of his feet.

“Follow me,” Lorne said, leading him down the wide corridor. A door opened ahead of them, Atlantis anticipating their needs before they needed them. John couldn’t quite make out what was on the other side.

“Now, it’s not completely ready yet, it’ll take some time to fill out, but…” Lorne grinned and shrugged a little, motioning for Sheppard to go first.

Try as he might to have prepared for whatever might be on the other side, his jaw still dropped open is glad surprise. It was easily the size of a hanger bay, with catwalks running back and forth across the length, and several stories up. Irrigation pipes were visible in the floors and walls. The whole thing had been very carefully constructed, accounting for optimal use of limited space. They were on the top edge of the tower, allowing sunlight to flood the room for a substantial part of the day, and there were sunlamps installed in the walls, no doubt for the times when direct sun was impossible.

“This is incredible,” John said. Two of the botanists looked up from the plants they were tending to and smiled at him. Most of the greenhouse was empty of both plants and people, but he knew it was only a matter of time before they had a substantial crop – assuming they could get the seeds the needed from their trading partners. “How long before it’s fully operational?”

“Hard to say,” Dr. Parrish said. “We’ve been collecting edible plant samples for a while, but it may take some time to build up sufficient crops to feed our population. Unless we get something more substantial soon, it may take up to a year before we are self sustaining.”

A year. A year was a long time to rely on trade for food, but it was so much better than having no timeline at all.

“Good work. Keep it up. Thank you for showing me this, Colonel.”

Atlantis had been relying heavily on Earth for six years, and it had been a long time since that first year, since they’d been left to fend for themselves. It was easy to forget how hard it had been, how difficult it was to find enough food to fill the tables, and now it was even harder. True, they’d made friends over the years, but they’d also made enemies. And now, with more mouths to feed, and less supplies to trade, it sometimes seemed impossible that they would make it through the month.

But this? This was promise. This was the future. They just had to hold out a little bit longer.

 

Fifty-six days after the end of the world, almost a month after Atlantis was granted autonomy, he still dreaded the weekly call to Helios Colony. The last few calls had coincided with political visits instead of updates with Sam or Jack. Despite this, Sheppard sat down near the dialing computer and called up the address. “Helios Base, this is Atlantis, do you read?”

“ _One moment, Atlantis_ ,” he heard a vaguely familiar voice respond. The video showed static for a few seconds before a face appeared. Sheppard didn’t know the name of the technician, but had seen him many times. He slid out of frame and was replaced by Sam, who was looking much more relaxed than he had last seen her.

“ _Good morning, John_ ,” she said. “ _Sorry I’ve missed your last few calls, we’ve been busy_.”

“Is it morning there?” he asked. “It’s nearly midnight here.”

“ _0800 here, though we have two suns, so it always feels like morning_.”

“Really? How’s that working out?”

“ _It’s definitely an adjustment. We only have about 4 hours of true darkness_.”

“Sounds exhausting. How goes everything… else?”

Sam smiled. “Rough,” she said. “ _Atlantis may be off the table, but there are still a lot of decisions to be made over here. The talks have been going non-stop for weeks. People have been planet jumping, trying to figure out which one best suits them. It hasn’t been going particularly well because no actual laws have been set down_.”

“Sounds like a pain in the ass.”

“ _Like you wouldn’t believe. How are things on your side of the river_?”

Sheppard shrugged. “I feel bad that they’re going pretty okay. We got our greenhouse set up just last week. Parrish tells me it’ll be a while before we have a significant crop, but we’re all a little excited.”

“ _They’re_  a little excited,” McKay said, suddenly appeared at John’s shoulder. “No one is taking me seriously when I remind them that meat doesn’t grow on trees.”

Sheppard laughed into his hand.

“ _Hi, Rodney_ ,” Sam said, a hint of a laugh echoing in her voice.

“Hi, Sam. How are you guys tackling the meat situation?”

“ _Um, well, Helios has a large population of a bison-like creature, and I’ve been told that Hyperion has several species of elk_.”

“Oh god, what I wouldn’t give.”

“Ignore him,” Sheppard said. “He’s just cranky because we also haven’t found an alternative to coffee either.”

“ _Ah. Daniel is suffering withdrawals as well_.”

Sheppard looked away from the screen for a moment as one of the technicians caught his attention. “Alright, I guess that’s the cap on our weekly dial-in. Any idea when Daedalus starts back this way?”

“ _They left four days ago_ ,” she said. “ _And_ boy _are the World Leaders pissed_.”

“Oh? Why is that?”

“ _Let me see if I can capture McLaughlin_ ,” she said, sitting up straighter. Her next words came out in a terrible mockery of an English accent. “ _They already have a flying city, why do they need one of our spaceships?”_

“Did anyone tell him that we can’t actually fly the city with the amount of power we have?” Rodney asked from off-screen.

“ _Yeah_ ,” she said, shaking her head. “ _I’m pretty sure they weren’t listening_.”

“That is so like them. Anyway, see you next week.”

“ _Bye_ ,” she said with a little wave. The gate shut down.

“Who would have thought we would be in the better situation?” Sheppard said.

“We wouldn’t be if it weren’t for my brilliance.”

“Rodney.”

“What? Fine. Lorne helped.”

John rolled his eyes, rolling his chair back. “Come on, Rodney. Let’s grab a snack. Maybe a game of chess.”


	5. Remain

“ _Colonel Sheppard, please report to the control room._ ”

Sheppard groaned loudly and grabbed his earpiece and a towel from the bench. “What is it, Banks?” he asked over the comm.

“ _Subspace transmission from the Daedalus_.”

“Hmm,” he said to himself as Ronon followed him out of the gym.

“I thought they were still on the edge of the galaxy,” Sheppard said, entering the control room two minutes later.

“They are, sir,” she said.

“Alright, let’s hear it.”

A video appeared on the viewscreen. “Colonel Sheppard, I realize I still have several of your people on board, but I’d like permission to make a small detour to a system near the edge of the galaxy. One of my scientists has been taking readings the past few trips, and would very much like to investigate while we’re out here.” The video ended.

“Prepare a response,” Sheppard said. When Banks nodded, he spoke into the computer. “Permission granted. Have fun, but don’t dawdle.”

“Maybe they’ll find an acceptable alternative to coffee,” he said as he and Ronon walked back down the steps away from the control room.

 

John didn’t hear much from the Daedalus for several days – just a few messages saying they’d found something interesting and were on their way back to Atlantis. He figured it must not have been that interesting, or they would’ve said more, asked to hang around a while longer.

He tried not to worry, tried not to let the impending sense of dread cloud him. Something was just on the horizon, he could feel it, as he had felt before. Sometimes he wondered if it was Atlantis herself who could sense things before they happened, and had somehow communicated it to him.

“Do you two ever sleep?” Jeannie asked, passing them in the commissary well past midnight. The hall was nearly empty, save a couple marines.

“Not really,” John replied, though he was, admittedly, tired. But he hadn’t slept a full night in months. He moved his queen’s knight up and to the left.

“Sleep is for the weak,” Rodney said, cackling as he overtook John’s rook.

“What are you doing up?” John asked.

“Bad dreams,” she said, shrugging her shoulders. “Thought I’d take a walk.”

“I’m sure Carson could prescribe something to help you sleep.”

She shook her head. “I’ll be okay. Though someone should consider drugging the two of you.”

“Oh please, just because I don’t keep the same hours as you, doesn’t mean I don’t sleep.”

“Checkmate,” John said with a smug smile.

“Hey! Where did that come from?” Rodney exclaimed.

Jeannie laughed as she walked away. Rodney pouted.

John leaned back in his chair and watched as Rodney reset the board.

“What?” Rodney asked when he caught John watching him.

John shook his head. “Nothing. I’m just tired.”

“Call it a night?”

“One more game. I’ll give you a chance to redeem yourself.”

“Oh, I appreciate that. Really.”

They played for several minutes before Rodney called him out on it again.

“What are you thinking?” he asked.

“Whether you’re going to move your bishop or knight,” John said.

“No, I mean… When you look at me like that. What are you thinking?”

“What?”

“What’s going through your head? Because sometimes I think… I don’t know. Forget it.” He moved his bishop.

“Sometimes I think about how annoying, how beautiful, how crazy you are.” He said it all so smoothly that Rodney almost thought nothing of it.

“What?” Rodney asked when finally he found his voice.

“ _Senior Officers to the control room_.”

“Ugh, what now?” Sheppard groaned as they got up, abandoning their game. Not two days ago they got the same call after an off-world team was attacked by the wraith. With six teams currently out, the chances were all too high that it was more of the same.

They found Caldwell in the control room, wearing an eerie grin, along with Zelenka and Lorne who were looking equally excited. Not quite the situation either had expected to find.

“What’s going on?” Ronon asked, appearing a mere moment later.

“You’ll want to pack a bag, Colonel,” Caldwell said. “That system my people wanted to take a look at? We found something.”

“An Ancient city,” Zelenka said, too excited to contain himself.

“What?” Rodney and John asked in unison.

Caldwell nodded. “It’s half buried, and from what we can tell, any ZPM that might be there are completely depleted, but she is of comparable size to Atlantis, and structurally intact. I thought you might like to check it out with us.”

 

The trip was nearly four days on the Daedalus, but the alternative was 12 days by jumper from the nearest ‘Gate.

“I did the calculations and compared it to the Ancient database,” Rodney said, lying down on the lower bunk. Guest quarters aboard the Daedalus were tiny, with only a few square feet not taken up by the small bunk bed and even smaller desk. “This planet  _did_  have a stargate, at one point. We tried dialing it our first year here, but couldn’t get a lock.”

“What happened to it?” Sheppard asked.

“Well, at the time we assumed that the outpost mentioned in the database had moved or been destroyed. Now that we know it  _is_  there, my guess is that the Gate is just buried. It’s the first thing I’m looking for when we get there, if only so we don’t have to spend  _four days_  getting back.”

Sheppard smirked. While he completely appreciated being out of contact with the other Earth colonies for a few days, he knew how much Rodney hated downtime. There was only so much work he could store on a tablet, only so much he could do without direct access to his lab.

“Just go to sleep,” he said, closing his eyes. “When you wake up, we’ll get breakfast, and then be there in no time.”

“I don’t know how you expect me to sleep with all this excitement,” he said. “Also, this mattress is a piece of shit.”

“Go to sleep, Rodney.” The mattresses were pretty shitty.

He could hear Rodney move around, trying to get comfortable in his admittedly lumpy mattress. A few minutes later, he set his tablet on the nightstand and turned out the light.

“Hey, Rodney?” John asked quietly a while later.

“Yeah?” By the sound of his voice, he wasn’t any nearer to sleep that John was.

“What’s the city called? Did it have a name?”

“Mm, yes,” Rodney said, sounding somewhere between annoyed and disappointed. “ _Nemora._ ”

“That’s not so bad.”

“It means forest.”

They tried to sleep for a while more before Rodney said “Are you still awake?”

“Barely.”

“Nevermind.”

“What is it, Rodney?”

“Well… you called me beautiful. Which is baffling. No one calls me beautiful. Well, my mother did, when I was a child, but I’m pretty sure that had little to do with any physical beauty and more to do with shutting me up, but-”

John found himself wishing, not for the first time in four days, that he’d instead bunked with Ronon or Zelenka – but Ronon hardly fit in the quarters by himself, and Zelenka’s brand of babbling was generally more harsh on John’s ears. “Go to sleep, Rodney,” he said, unable to keep a fond smile from forming on his face.

“I just wanna know…”

“Not now,” he said, which Rodney took to mean something more like  _not ever_.

Like hell.

 

 “You said there were no discernible energy readings until you were right on top of the planet?” Zelenka asked as they made the final approach. “What led you here in the first place?”

“The blue star at the center of this system drew the attention of Dr. Lindsay. To be honest, I wasn’t really paying attention. On the way in, we detected trace energy readings and decided to check it out.”

The blue star itself was no doubt fascinating, and Rodney thought he’d like to take a look at it, or at least get some information from Dr. Lindsay. But the planet was of more interest.

“Breathable atmosphere,” Rodney announced from the information on display. “Surprisingly dense ozone layer, lots of fresh water. No lifesigns bigger than a cat. Looks, dare I say it, cozy. Did anyone scan for Naquadah?”

“Yes sir,” Meyers said, typing rapidly. “Nothing major anywhere on the planet, but there is a small concentration near one of the buried sections.”

“Damn,” Rodney said, looking over her shoulder.

“What’s the matter, Doctor?”

“It’s the stargate. It’s going to be harder to get to than I anticipated. You have combat engineers aboard?”

“Of course,” Caldwell said.

“We’ll need them.”

 

The city was on a beach – no doubt many millennia ago it was floating in the ocean  _near_  the beach, but in the time since, much of the water had evaporated, leaving the city in sand. Nearly half the city had been overrun by trees, and when glass broke, the halls had filled with sand and mud.

A large team beamed down to the surface: McKay, Zelenka, Sheppard, Ronon, Caldwell, combat engineers, a dozen Daedalus scientists, as well as a few marines.

“There is no front door?” one of the scientists asked.

“The cities were designed to sit on water when they’re not flying through space,” Rodney said, inflected with his usual annoyance. “I’d hazard a guess the Ancients weren’t expecting many people to _walk_ up.”

“Secondary jumper bay,” Sheppard said, already walking in the direction he knew the bay to be. His P90 was drawn low, but he didn’t expect to meet any trouble.

“Of course, it’s the lowest point of access. Ours is usually underwater.”

It only took a few minutes of walking, followed by ten minutes of struggling to get the bay doors open, before they were finally inside. A dozen Jumper sat silently in their spaces.

“These are going back to Atlantis,” Sheppard said with a grin. He jogged over to one, opened the back hatch and sat down in the pilot seat to check that it was still operational. It hummed to life immediately, and his grin grew wider. Atlantis was down to only a handful of Jumpers, having more was like a miracle.

“At the very least this trip will give us an ample supply of spare parts,” Zelenka said as Sheppard rejoined them on their way into the city.

“Oh please,” Rodney said. “This city has  _so much more_  to offer.”

“I said,  _at the very least_. Do you not listen?”

 

Rodney expected to find the power distribution center with three dead (or, if the universe was on their side, not quite dead) ZPMs. Instead there were none.

“Is this a problem?” Caldwell asked.

“Well, no, I can still tie our naquadah generator in. It’s just surprising.”

“Perhaps the Ancients brought them when they abandoned this city,” Zelenka said, as they got down to connecting the generator.

“Hmm. Maybe.”

“How long?” Sheppard asked.

“An hour,” Zelenka said, just as Rodney was saying “Twenty minutes.”

Sheppard rolled his eyes and motioned for the rest of the group to follow him. Most of the doors around the city were closed, and with no power it took some force to get them open, but they could work their way to the control room, and hopefully power would be up soon (he knew from experience that even Rodney’s estimates tended to be exaggerated).

“ _Colonel Caldwell,_ ” Meyers said over the comms. “The combat engineers have uncovered the stargate. Shall I beam it directly to the gateroom?”

“Not yet, Major,” Caldwell replied.

The tower started to light up before they reached the control room.

“All clear,” Sheppard said.

“Major Meyers, feel free to drop the gate in.”

A moment passed, then the gateroom filled with light. When it dissipated, the Gate was sitting in its rightful spot.

“Feels almost like home,” Sheppard said. He started turning on main systems, which the scientists were giddy to start examining.

“Sir, we’re broadcasting some kind of frequency,” Dr. Lizer said, furrowing her brow.

“Shut it off,” Sheppard and Caldwell said at once.

“I’m not sure how. It doesn’t appear to be Ancient, but came online when the power did.”

“Figure it out.” Sheppard tapped his earpiece. “Rodney, get your ass to the control tower.”

“ _On my way._ ”

He appeared less than a minute later. “What’s going on?”

“We’re broadcasting an unknown signal,” Lizer repeated. “I can’t figure out how to shut it off.”

“Get out of the way,” he said, sliding her chair to the side. “Oh no… Nono no.”

“What is it, Doctor?”

“It’s Wraith. Probably been here for thousands of years. They couldn’t do anything with the city on their own, so they set up a beacon to start broadcasting in the event that someone came in and turned the power on.”

“Turn it off!” Sheppard said.

“I did! But that won’t matter if someone was close enough to hear it.”

Caldwell tapped his earpiece. “Daedalus, please keep an eye out for any Wraith who might have heard that.”

“ _Yes sir_.”

“And while we wait for shit to hit the fan, why don’t you check the Ancient database for anything interesting,” John said, starting up the stairs.

“What are you gonna do?” Ronon asked.

“Check that the jumpers are fully operational, in case we need them. Someone should dial Atlantis and have them send us a few people with the Ancient gene to fly them back.”


	6. Discovery

Finding an Ancient city was a stroke of luck they could never have anticipated, and John knew better than to hope that the Wraith wouldn’t come to investigate the signal. He was disappointed, but not surprised when a Wraith ship dropped out of hyperspace in orbit of the planet.

“ _Sir, we have Wraith. Shields are holding, but our weapons have been damaged. We’re unable to fight back._ ”

“Give me two minutes,” Sheppard shouted. He closed the rear hatch of the Jumper he was in – thankfully one that was not missing any key systems.

“ _What are you doing_?” McKay called over the comms. “ _You can’t possibly be thinking about taking on a hive ship on your own._ ”

“Don’t have much choice, do I?” he replied.

The flight felt longer than it should have, even with pushing the engines to their max.

“ _If you go any faster, you’ll burn out the engines before you get there_ ,” Rodney said.

“They’ll be fine, McKay,” he said.

As he made the final approach, he could see the sporadic fire from the Hive – enough to wear down Daedalus’ shields eventually, but certainly not full capacity. The Wraith ship hardly looked battle worthy. He crossed his fingers and hoped that their shields were among the damaged systems.

He flew right up to the dart bays, well beyond the point where a shield should’ve been, dropped his cloak and began firing.

He didn’t remember much after that.

 

Nemora was old, nearly as old as Atlantis herself, and nearly identical in structure. The contents of her database could not be more different – only the early history of the Ancients was the same.

She had spent most of her existence in the vastness of space, seeding viable planets with stargates, before finally settling down at the edge of the galaxy. Like Atlantis, her people had set up hundred of research labs, running a whole host of interesting, if not overconfident, dangerous experiments. Rodney suspected that any race who managed to live as long as the Ancient had would eventually run out of logical, practical studies and would move on to everything else the universe had to offer.

Eventually, some 70,000 years before the fall of the Ancients, they abandoned the city, though for the life of him he could not figure out why. There was no mention of the Wraith in their history files, and any other enemy they had (he’d found reference to a race called Qinarins, who seemed to be at odds with the Nemorans), were little more than a nuisance, not a significant threat.

Rodney looked over the unconscious form of Sheppard, as if hoping to find some answer there. There was none.

 

He was barely awake when Rodney’s voice loudly interrupted any chance of falling back to sleep.

“I hope you understand that you’re keeping me from valuable work.” He was sitting in the chair next to Sheppard’s bed, in what looked to be the Daedalus infirmary.

“Hmm?” John groaned. “How long have I been out?”

“Four agonizing hours,” Rodney said.

“Wraith?”

“You successfully destroyed the hive before knocking yourself unconscious. It might be considered impressive, if you weren’t so stupid. And no, there is no indication that any other ships heard the call. We should be in the clear.”

“Good,” he said, trying to sit up. His ribs disagreed.

“You’ve got three cracked ribs,” Rodney supplied. “And I  _distinctly_  recall agreeing that you wouldn’t pull any more stunts like this.”

“It wasn’t a suicide run, Rodney. I had ever intention of making it back unscathed.”

“Good. You’re still an idiot, and we’ll talk about it when we get back to Atlantis.”

John smiled. Rodney sounded exactly like his mom had whenever he’d gotten into trouble at school.  _We’ll talk about this when we get home_.

“Let’s get back down to the planet,” Rodney said. “We found some really fascinating stuff while you were napping.”

“I’m sure you did. Ow.”

“Hey, this is entirely you’re fault,” Rodney said, helping him to his feet, careful to avoid his injuries.

“Yes, because  _I_  called the Wraith here.”

“Well, no, but you did decide to fight them singlehandedly. Like you always do.”

“How ‘bout instead of yelling at me, you just tell me what you’ve found,” he said, batting Rodney’s hands away. He only half listened as Rodney babbled the whole way to the transporter room.

 

Given the size of Nemora, there was no way they could explore everything – they hadn’t even explored all of Atlantis. After the initial couple of days, they agreed to put it on the backburner. They’d scavenged a few crates full of parts, took every jumper, downloaded as much of the database as they could store, then left the city alone once more.

“What are these?” Sheppard asked, opening one of the crates. It didn’t look much like spare parts, but then, he didn’t know the inner workings of the city like McKay did.

“Non-lethal energy weapons, mostly. If we can reverse engineer them, we can offset our reliance on our ever dwindling supply of bullets.”

“Cool.”

“Thought you might think so.”

“You gonna sleep anytime soon?” Sheppard asked.

“Wasn’t planning on it.”

“Rodney.”

“I’m not tired. And with some of these parts I might  _finally_  be able to get the ZedPM seeder up and running.”

“ZPM seeder?”

“Yes, it makes ZedPMs. It was almost completely trashed when we got here.”

“Why haven’t I heard anything about this before now?”

“Because I couldn’t do anything to fix it and there was no point in getting anyone’s hopes up.” Of course Rodney’s arrogance wouldn’t allow him to mention anything that would potentially undermine his perceived intelligence.

“But now you can fix it?”

“Maybe.”

“Hmm. That’s excellent. You still need to sleep.” He was pretty sure he hadn’t slept any of the time they’d spent on Nemora.

“Yes yes.”

“Rodney. If you’re still here by midnight, I’ll send Carson in with a sedative.”

“Whatever.” He wasn’t paying attention.

Twenty minutes later he dropped everything he was doing and left the lab in search of Sheppard.

“Ah, there you are,” he said, finding him walking out of the gym. Rodney looked around, but found no sign of Ronon or Teyla or any of the Marines he sometimes sparred with. “Been looking all over.”

“What’s up?”

“We need to talk.” Which of course was the absolute worst thing to say, and Rodney knew it the moment Sheppard’s body tensed. “Not about your proclivity for suicidal heroics, though that is something we should talk about, and you should stop doing. Seriously, I don’t know how many times a person can think their best friend is dead before they  _snap_. But no, I want to talk about what you said in the mess the other night.” Which didn’t easy any of Sheppard’s tension.

“I don’t know what you’re talking about.”

“Bullshit. You called me beautiful. And then you spectacularly and conveniently avoided the topic for a week.”

 “Rodney, don’t,” he said. “Just. Forget it, okay?”

“No.”

“Rodney-”

“Stop saying my name like that.” Like it hurts.

“What do you want me to say?”

They were standing close, closer than John could bear. “I don’t know. Something.”

“I shouldn’t have said anything.”

“But you did.” Rodney’s hand came up to his face. John almost shied away from the contact. Almost.

“What are you doing, Rodney?”

“Thinking about kissing you. Pretty serious about that thought. Not sure how you’ll respond though. I’m quite good at misreading these things. Maybe you could tell me, clear things up a little. What would you do if I kissed you?”

“I’d kiss you back.” Rodney thought he sounded almost angry, like he’d found something he wasn’t supposed to find, wasn’t permitted to have.

So Rodney kissed him, soft at first, tentative. Like testing the waters. But John did just as he said he would, pushed back harder. He wrapped his fingers around Rodney’s biceps, pulled him closer.

“And if I brought you back to my quarters. What would you do then?”

“God, Rodney, don’t ask me that.” His lips were pink, and his eyes were closed. Rodney wondered if he was deliberately making it difficult to read him.

“What would you do?” he asked again, more forcefully.

“I’d take every inch of you, if you’d let me,” he said, his voice low and gravelly.

Rodney kissed him again. “Is that a promise?” He felt a rumbling in John’s chest, something almost like a growl, and it made Rodney grin. He tugged on John’s sleeve, pulling him toward the nearest transporter.

It was late, and Atlantis was quiet, but Rodney counted it as a blessing that they ran into no one between the transporter and his room.

“You really wanna do this?” John asked as the door closed behind them.

“God yes,” Rodney said.

John took a step back, forcing distance between them. “I’m serious. I can’t do casual sex with you, Rodney.”

Rodney didn’t think he’d ever seen him so open before, never seen him without the walls he’d carefully built. But they were gone, completely crumbled, and all that was left was John, looking full of lust and need and dread and fire.

He didn’t think he had the words to tell him that would make him believe, so he settled for kissing him, holding on to him, pulling him as close as he can. “I want this,” he said, hoping it was enough.

 

They lied in bed, shoulder to shoulder, feeling equal parts calm and exhilarated. Rodney danced his fingers across John’s bare thigh, thinking vaguely about quantum entanglement.

“How long…” Rodney didn’t finish the question, but he didn’t need to.

John rolled on his side to face Rodney, then kissed his collarbone. “Always. I always wanted this.”

“Jeannie was right. We are the biggest idiots on Atlantis.”

“Ironic coming from the biggest genius on Atlantis. Why are we idiots?”

“We have wasted  _so much time_. Like, seven years. That’s seven years of orgasms I’ve been missing out on!”

John laughed, and it was the most beautiful thing. “I’m sure we’ll make up for it somehow.”

“You’re damn right.”

“Hey, this is not my fault. How was I supposed to know you were interested?”

“How could I not be?”

“You were with Katie, then Jennifer, both for quite a while. I jumped to the not-unlikely conclusion that you were straight.”

“You were married to a woman!”

“And there were good reasons it didn’t work out.”

“Such as? Did you use all her hair product? Or was she concerned that you were part elf? Interspecies relationships can be hard.”

John swatted him with a pillow. “It may have had something to do with my being more interested in men than I was in her.”

“Hmm. Her loss.” He kissed John softly, then rolled over to go to sleep.

“You’re thinking too loudly,” John said a few minutes later. He pressed a kiss to the spot between his shoulder blades before Rodney rolled over again.

“Sorry, I’m on the verge of a mathematical proof and it’s driving me crazy.”

John grinned. “I kinda like math.” Which Rodney knew, of course, but hadn’t considered it like this. “Talk me through it.”

 

Rodney didn’t know how long he sat in the commissary, working over a half-eaten tray of food, before he realized Ronon was sitting with him.

Rodney looked up. “Hmm?” He hadn’t heard a word he’d said.

“You’re too quiet,” he repeated. “It’s unnerving.”

“Coming from Mr. Tall, Dark, and Silent?”

“You always talk, McKay,” he said. “Even if no one is listening. Why not now?”

Rodney waved him off. “I’m deep in thought. Hush, you’re ruining my focus.”

Teyla sat down to Rodney right a while later, and she too started shooting him looks of concern. “You are exceptionally quiet today, Dr. McKay,” she said eventually.

“You hate it when I talk, you hate it when I don’t. Make up your minds!”

“Would you not be concerned if Ronon or myself suddenly began behaving out of character?” she asked.

“Well, yes, but. Look, I’m working on a math thing. I could talk to you all about it if you’d like, but doing so would greatly reduce the speed at which I am working. Not to mention it is so complex that I’m not even sure I  _can_  dumb it down to a point that you could understand it.”

“You know what, quiet is okay,” Ronon said, as Sheppard sat down next to him.

“What’s up, guys?” he asked, stuffing something squash like into his mouth.

“Rodney was behaving strangely; when Ronon and I voiced our concern, he grew annoyed.”

“I’m always annoyed.”

John shot him a smile when Teyla and Ronon weren’t looking, and whatever annoyance he had with them dissolved. Because apparently he had the emotions of a teenage girl.

And Jeannie knew  _immediately_. She sat down on Rodney’s other side, started to say something, but stopped. She narrowed her eyes at him, studying him for a moment, then looked at Sheppard, who was happily eating his mystery vegetables.

“Ha!” she exclaimed, surprising everyone. “Ha!”

“What are you- would you stop that?”

“Ha!” she said again, then roped her arms around him and squeezed.

“What is going on?” Ronon asked.

“Jeannie seems to have realized something significant,” Teyla said.

“Well, yeah,” Jeannie said, grinning madly.

Teyla turned her attention to John, hoping for some kind of explanation, but found him pointedly not paying any attention. Though if the generally pleasant look on his face was anything to judge by…

“Oh,” she said, a smile growing on her face.

“Oh what? I don’t get it.”

She raised her eyebrow at him, looking between McKay and Sheppard a couple times.

“Oh that. It’s about damn time.”

“What are you guys talking about?” Rodney asked, completely oblivious.

“They know, Rodney,” John said. If he was bothered by it at all, he didn’t show it.

“Oh. Well. This just got infinitely more uncomfortable.”

“Why? Is it not good news?”

“Well, yes, but.” But what, he didn’t know.

“We’re all just excided for you, Mer,” Jeannie said.

“Hey wait, what do you mean, ‘it’s about time’? How long have you known?”

Ronon shrugged. “Six years?”

Rodney’s mouth fell open. Ronon had only been on Atlantis for six years. “Did no one think to, I don’t know,  _say something_.”

“No.”

“It is not customary for my people to meddle in matters of the heart.”

“Dr. McKay,” someone said, approaching their table.

“Oh thank god. What is it, Dr. Parrish?”

Parrish sat down next to Ronon, carefully avoiding contact. “I’ve been thinking, and then I did some digging in the Nemora’s database, and, well. Where did their food come from? They spent thousands of years in space, which of course must have meant using up dozens of ZPMs, but they would have had no permanent land on which to grow food-”

“Get to the point faster please.”

“The database implies that their greenhouses and hydroponics are significantly more advanced than ours. They would have to be, in order to supply that much food for such long periods of time. I would like to go to Nemora and investigate further, hopefully transfer some of their technology back here. It might greatly increase our yield.”

“Will it give us coffee? Or meat?”

“Rodney,” John said in a warning tone.

“Yes, yes, I’ll approve the mission, if he does,” he said, jabbing a finger in Sheppard’s direction.

“I’ll approve any mission that increases my chances of ever seeing a tomato again,” he said with a nod. “Take Lorne’s team, tomorrow afternoon.”

Parrish grinned and excitedly jumped from his seat, bumping Ronon slightly. “Thank you both!” he said before running away.

 

John realized, a little too late, that all the business with Nemora (and Rodney), had caused him to ignore parts of his routine. When he finally got around to dialing Helios, he was immediately met by Sam’s face.

“Expecting my call, were you?” he asked.

“ _Actually, I just finished up with the commander of Hyperion base. Your call is two days late_.”

“Sorry about that. We had a busy week, it slipped my mind.”

“ _Oh, anything exciting?_ ”

“Yes, actually, but you have to promise not to tell the World Leaders.” The last thing they needed was those guys trying to get their hands on Nemora.

She crossed her heart with her index finger, then sat forward in her chair excitedly. He told her all about the Nemora and their trip.

“Hi, Sam,” Rodney said, leaning over Sheppard.

“ _Hi Rodney. John was just telling me the good news_.”

Rodney blanched, and practically jumped backward. “Really. I… what?”

“The  _other_  good news, Rodney,” he said with a hint of amusement.

Rodney’s eyes widened. “Oh. Yes. Very exciting.”

John watched as Sam’s face grew into something that could only be described as gleeful. “You guys… Really? Congratulations.”

“Yes, well, not so loud with that, maybe?”

Her grin only grew wider. “Alright, I’ve got to go. I have a team due back in a few minutes. You kids behave yourselves.”

Rodney followed Sheppard into his office a few minutes later. “I’m sorry. I didn’t mean to… you know.”

“It’s okay,” John said.

“And I didn’t mean for Jeannie and Teyla and Ronon to find out either. It just… happened.”

“It’s okay,” he said again.

“Really? Because I know how your military is and I don’t want you to get in trouble.”

“Rodney, I have no superiors. I am the Supreme Commander of Atlantis. Who exactly are you expected to court marshal me?”

“Well, I guess you have a point there, but your men will start a mutiny or something when it gets around – which it will because apparently secrets don’t exist here.”

“There is no law in the Lantean Armed Forces that says two men cannot be together.” There were codes on consent, relations between commanding officers and their subordinates, sexual harassment, and even harassment based on religion, race, or sexual preference, but nothing that even looked like the former ‘don’t ask don’t tell’.

“Oh. Really?”

John nodded. “It was among the first things Lorne approached me on when he was developing the new code. Members of former non-US services also agreed, and so far, no one has complained. I don’t expect anyone will.”

“I didn’t know that.”

“I’m not saying that we should go around flaunting it.” But he wasn’t one to flaunt  _any_  kind of relationship. “But it’s okay if people know.”

“You’re not seriously calling yourself Supreme Commander, right?”

“Isn’t your team leaving in twenty minutes?” Sheppard asked. He and Jeannie were tagging along with Parrish and Lorne to do some more digging around Nemora.

Rodney jumped from his seat. “I almost forgot.”

He was halfway out the door when the gate activated.

“Who is it?” Sheppard asked, jogging out. Only two teams were out, neither do back until tomorrow morning.

“Receiving Teyla’s IDC,” Banks said.

“Let ‘em in.” He walked down the steps to meet Teyla and Ronon, who walked through the gate unharmed. Both were looking more than a little irked. “You’re back early,” he said.

“The Ellowrans are,” Teyla paused, looking for the most diplomatic word.

“Assholes,” Ronon supplied.

“Particular,” she said, diplomatic as always. “They are only willing to discuss trade negotiations with the leader.”

“You explained that you’re in charge of all trade negotiations?” he asked, though he already knew the answer.

“Of course. But I suspect that they also took issue to my being a woman.”

“Ah. We’ll just have to move to the next on our list.” He didn’t want to get involved with a government that exhibited such dramatic sexist tendencies.

Teyla shook her head. “The Ellowrans have much of value to us. I think it would be unwise to overlook them. They have plentiful crops and appear to ask little in return. I think we could benefit greatly if you were to return and handle the negotiations yourself.”

 

He suited up and made his way back to the gate just as it was dialing Nemora.

“You’re going too?”

Sheppard shook his head. “Ellowra. Things didn’t go well with Teyla, but she seems to think I can do a better job.” The wormhole engaged. “Careful out there,” he said to Lorne. “Have them back by dark.”

“Yes, sir,” Lorne said.

He waited off to the side with a team of Marines, while the technician dialed Ellowra. “See you in a couple hours,” he said, waving up to Teyla.

The Ellowran settlement was less than half a click from the gate, but a representative was waiting for them at the treeline.

“You are Colonel Sheppard? The leader of your people?” the young man asked.

“Yes,” he said. “And you are?”

“Tarrik. I will lead you to Chancellor Galbor.”

They walked in silence to the settlement, and met Galbor on the steps of a large building. He was a sizable man, older than Sheppard had expected. He reminded him a little of depictions of Santa.

“Welcome, Colonel Sheppard. We are pleased that you could join us. Come inside.” Sheppard stepped in, but when the Marines made to follow, they were stopped by a pair of guards.

“I’m afraid we do not allow outsiders into the chamber,” Galbor said. “You and I will discuss trade in private.”

“Sir,” Sgt. Seaver said, clearly disagreeing.

“It’s fine,” Sheppard said. “Just don’t wander off too far.”

Seaver started to object again.

“I recognize your concern. You’ll be on radio the whole time. If anything goes wrong, you’ll rescue me. But nothing is going to go wrong, because the Ellowrans are peaceful people.”

“Of course,” Galbor said. “We have no intentions of harming you.”


	7. Rescue

**Notes for the Chapter:**

> I fucking love Teldy and her team, and I am so upset that we only see them ONCE. Anyway, they make a small appearance here (and might get their own story in the series, eventually). For the purposes of this story, sometime after Vega's death in Whispers, Cadman joined the team in order to keep things awesomely girl-powerful.

Two minutes to 1900 AST had Teyla tapping her foot impatiently.

“They are not yet late,” Zelenka said.

“I know.”

“They will return. Rodney always waits until he can wait no more.”

“I know. Is Ronon ready?”

“Yes,” Ronon said from somewhere behind her.

“And Major Teldy’s team,” Zelenka relayed to her once more.

The gate activated.

“Receiving Colonel Lorne’s IDC.”

Teyla nodded to lower the shield, then followed Ronon down to the gateroom.

“What’s going on?” Lorne asked, spotting Teldy’s team.

“Colonel Sheppard was due back many hours ago,” Teyla said. “We radioed in and received no response, from neither him nor Sgt. Seaver’s team.”

“Did someone go looking for them?” McKay asked.

“Gee, wish we’d thought of that,” Mehra said, handing him a tac-vest and P90.

“We went in a few hours ago,” Teldy said. “Made the Ellowrans real uncomfortable, but there was no sign of any of our people. They claim Colonel Sheppard left at the end of their negotiations and headed for the gate.”

“Something tells me you don’t believe them,” Lorne said.

“I don’t trust anyone that’s made that uncomfortable by a pair of breasts.”

“You’re returning to investigate further,” Teyla said. “It should be past nightfall. Hopefully that will afford you to uncover something.”

 

“I already gathered the last 42 addresses dialed,” Dr. Porter said as they stepped through the gate. “Several were familiar, trading partners of our own. They’ve already been contacted; no one has heard from our team.”

“If we have to search them all, it’ll take months,” Cadman said.

“Someone here must know something,” Rodney said.

“We should split up,” Ronon said.

Lorne nodded. “Teldy, your team can start at the tree line. Grober, go with Ronon and McKay, take north of the gate. Eeder, Rosk, and I will head south.”

 

“This is unusual,” Lorne said, running his fingers over the old stone temple.

“What’s that sir?” Eeder asked over his shoulder.

“I’m not sure,” Lorne said. He was neither a linguist, nor an anthropologist, and while his team was smarter than most marines, they weren’t scientists either. He clicked his radio on. “Hey, McKay?”

“ _They’re Wraith worshippers_ ,” McKay said loudly over the radio, confirming Lorne’s suspicions. The temple was Wraith.

“What did you find, Doctor?” Lorne asked.

“ _There’s a temple out here, well maintained._ ”

“We found something similar out here.”

“ _We got one too,_ ” Teldy informed them.

“ _This is very, very bad._ ”

“You think they might have called the Wraith when Sheppard arrived?”

“ _It’s no secret we come from a city of the Ancestors. They may have had standing orders to kidnap our leader if we ever found our way here._ ”

This information did not help them any – in fact it only made their search harder. If the Wraith  _had_  taken Sheppard and Seaver’s team, they had likely done so in a Hive, leaving no way of tracking them.

The only bright side Lorne could find was that they were likely still alive. The Ellowrans wouldn’t have sent Teyla away the first time if they simply wanted to feed. They had waited for Sheppard. They needed him.

 

“Where are you taking me?” he asked. His arms were bound behind his back, and he’d been stripped of all his tactical gear, but the Wraith who’d captured him showed no signs of feasting. Instead he’d sat him down at one end of a long table, invited him to talk and eat. The whole situation reminded him a lot of his first encounter with the Wraith, of Sumner’s meeting with the Queen. It all made his stomach uneasy. Sheppard didn’t touch the food.

“I have waiting a long time,” the Wraith said. “Finally my prize is within reach. Thanks to you.”

Sheppard had no idea what that meant. “Doesn’t the queen usually sit there?” he asked.

“This ship has no queen. We have long been without one. We prefer it that way.”

“Huh.” That might explain why the Ellowrans were so distrustful of women – if in fact they only worshipped this one particular hive.

“The Ellowrans have followed us for many generations,” the Wraith said, no doubt having read his mind. “They sacrifice a few to sustain us each time we rise from hibernation, but their numbers are allowed to grow under our protection.”

Sheppard didn’t need to hear about their  _noble sacrifice_. “What do you want from me?”

“You were recently on the edge of this galaxy, where you found an Ancient city. We were alerted to your presence. Our brother ship was sent to investigated, but never returned. Which could only mean that an Ancient had returned and was able to defend it, even despite its lack of power.”

“How could you know that?”

“We took the power modules,” the Wraith said. Dylan, he decided to call him in his head. “Many thousands of years ago, when we first discovered the city. We were unable to access most of its equipment, but set an alarm to go off when someone returned power to it. This I’m sure you know.”

“And?”

“We want the city for ourselves. Its technology is great, but we are unable to do anything without your assistance.”

“Surely you know that I won’t help you,” he said.

“Of course you will,” Dylan said. “We just have to find the right incentive.”

 

The Ellowran homeword was located near the edge of the galaxy, but still, with the inefficiency of Wraith hyperspace, Sheppard and his marines spent nearly a day in a cell. Occasionally, one of their guards would drop off some food, but he knew better than to eat any of it.

“Come with me, Sheppard,” Dylan said, opening the door to his cell.

“I won’t help you,” he said.

“You will. Or I will kill your people. Two of them will remain up here, and two will join us, to ensure that you remain on best behavior.”

Sheppard allowed himself to be dragged down to the Dart bay along with Seaver and Blake.

“Still think this was a good idea?” Seaver asked.

“Oh, you know how it is. You win some, you lose some.”

“Just say the word, sir.”

“Don’t do anything stupid,” he said. He hoped it translated to  _I have a plan_ , which he did not, but he did have the makings of a plan. Whether or not it was a good one would remain to be seen.

 

The dart spat them and a half dozen Wraith out on the surface of Nemora, near the very edge of a pier.

“Which way to the control center,” Dylan asked.

“Man, I have no idea,” Sheppard said.

Dylan pulled a stunner on Blake. “Which way to the control center?” he asked again.

“That way,” Sheppard said, stepping between the stunner and the Marine. He pointed off toward the center of the city. “That way, eleven levels down.”

“Good.” They started walking, and Sheppard felt one of the others nudge him with a stun rifle, pushing him forward.

“You do know the city has no power, right?” Sheppard asked, hoping this fact might somehoe slow them down.

“One of our brothers is installing the power modules as we speak.”

“Oh. What exactly is your plan here?”

“You will show us how to operate the city functions, then we will fly it to our homeworld.”

“I’m guessing we die somewhere in there?” Sheppard wasn’t even sure the city _could_ fly. It had been pretty weathered over the millennia. If it had been space worthy, Rodney would’ve mentioned as much, wouldn’t he?

Dylan did not respond.

“Right, so I should mention that Ancient cities are designed specifically to keep your race from being able to operate it. I wouldn’t even know where to begin on getting rid of those safeguards, assuming it’s even possible.”

“You will figure it out.”

“Yeah, see, I’m not a scientist, I’m a pilot. You grabbed the wrong team. Blake here is also a pilot, and Seaver is a weapons specialist. The guys you left on your ship like to hit stuff. None of us are scientists. Maybe if you let me call my people, they could send someone more capable-”

“More likely they will send reinforcements. No, you will get the ship operational. If not, you will fly it for us.”

He could feel the moment the ZPMs were reconnected the the city, felt her hum to life, like taking a huge breath of air after returning to the surface of a pool.

 “Got a plan yet, sir?” Blake asked quietly. Sheppard shrugged. Not much of a plan.

“The control center?” Dylan said, nudging him again.

“Yeah, yeah, this way.” He led them further, until finally they reached the control room. “Most of the city systems can be accessed from here,” he said. “But like I said before, it’s all designed to keep you out.”

After careful examination of the controls, one of Dylan’s underlings said something incomprehensible in Wraith, and Dylan smiled eerily. “It seems your own efforts to make this city more accessible to your equipment has opened the door to interphase ours.” He turned his attention back to his scientists and spoke to them in Wraith for several minutes. “How do we activate the city’s space flight?” he finally asked Sheppard.

“Hmm. You know, I’m not really sure. I have people who deal with these things for me.”

“I have warned you not to play games, have I not?” Dylan asked, pulling his weapon on Blake and firing before Sheppard could stop him.

“See, now I’m definitely not going to help you,” Sheppard said, carefully masking the angry that was growing.

“’m okay, sir,” Blake said from the floor, groaning loudly.

“How do we access the flight drives.”

Sheppard flared his nostrils and started down the nearby stairs. It was a long walk to the base of the tower, but it gave him time to think though his plan. The chair room was identical to the one in Atlantis, but felt somehow different. “The chair requires the Ancient Gene to use. We’ve never found a way to link our computers.”

“Then by all means, have a seat. If you try anything untoward, I will not hesitate to kill Mr. Seaver here.”

Sheppard sat down, activating the chair effortlessly.

 _Hey there, beautiful,_  he said to Nemora.  _I’m a friend of your sister. I’m hoping you can do something amazing for me._

Nemora cooed at him, and he almost laughed.

_Sorry, my heart belongs to another. But I won’t leave you here, so long as you can help me out of this jam._

A series of commands appeared in his mind, ones he’d never seen in Atlantis.

“Seaver?” he asked aloud. Seaver took a couple steps toward him. The Wraith moved to do the same, but did so a half second too late. Ten thousand volts came up from the floor, running the current through them all. The Wraith spasmed wildly for almost a full minute before Sheppard shut off the current.

 _Thank you_ , he thought at her.

“That was cool,” Seaver said. “What about the ones in the control tower?”

Sheppard brought up an image of the control room in real time. Four Wraith remained there, working on the computers, while Blake was still lying on the ground. “Think you can take them out?” he asked.

Seaver smiled and plucked several weapons off the dead Wraith around them. “Happy to,” he said, then jogged away.

  _Now onto the next task. There is a Wraith ship in orbit. I would like to destroy it, but I have people aboard. Any ideas?_

And apparently miracles did exist, because Nemora had something Atlantis didn’t. Beaming capabilities not too dissimilar to the Asgard’s.

 _That’s incredible. Perfect. I need you to lock on to something that looks a bit like this_ ; he sent her a mental image of the signal produced by the subcutaneous transmitters.  _And bring them aboard._  He could almost feel the beam pull his people down to Seaver’s location.  _Excellent._

Seaver’s voice came over the city-wide communication. “All the Wraith have been taken out, sir. Wallace and Jones are here, I assume your doing?

“You assume right. Listen, subspace communications are down. I need you to dial Atlantis and inform them of the situation.”

“Yes sir.” A few moments passed before Blake’s voice spoke.

“I think the Hive realized something happened. They’re locking weapons on us.”

 _Shields up. Weapons?_  He was able to fire off a couple dozen drones, but it was all she had in her arsenal. Barely enough to take out the ship.

“The Hive has been taken out,” Blake informed him over the radio. “Dialing Atlantis now, sir.”

“Have them send a team of marines, scientists and technicians. How are you feeling, Blake?”

“Fine, sir.”

“I’d like to have Beckett confirm that. As soon as the marines arrive, you and you team are to return to Atlantis.”

“I don’t think that’s necessary-”

“It’s an order.”

“Yes sir.”

Sheppard reverted his attention to the control systems of Nemora, getting lost in the mainframe. He didn’t know how much time bad passed before -

“What the hell do you think you’re doing?” Rodney exclaimed, walking into the chair room. “We’ve been freaking out, and you couldn’t even be bothered to make the call to Atlantis yourself? And what the hell happened to your eye?”

“Dylan didn’t like my smart mouth,” John said, sitting forward in the chair.

“Who’s Dylan?”

John waved in the direction of one of the dead Wraith.

“God, you’re an idiot,” Rodney said, kissing him.

“It’s not like I got kidnapped on purpose.”

“No more leaving Atlantis. If people are unwilling to negotiate with Teyla, they can shove it. Although, if Parrish’s estimations are at all accurate, we may not have to barter for food ever again. But no, you once again single-handedly took on a Wraith ship, and somehow won. Care to tell me what you’re still doing here?”

“Pre-flight.”

“Pre… are you serious?” Rodney quickly moved his focus to the tablet he carried, manually running through everything John had already been through.

“I want to move her,” he said. “She’s an awfully good beta site, and I don’t want any other Wraith coming back for her.”

“Is Atlantis going to be happy about this affair you’re having with her sister?” Rodney asked, frowning.

“Relax, Rodney, they both know I love you most. Now, her star drive, shield, and life support are fine, but communications are completely fried, and she’s out of drones. I don’t wanna get stuck somewhere without either. How long would it take to fix her up and find a new place to put her down?”

“Probably a couple hours at most,” he said. “And I think I already have an idea of where to put her.”

“Oh?”

“Horrendous hurricanes every twenty or thirty years, intense solar energy every few thousand, and the absolute last place anyone would look for her.”


	8. Epilogue

Ninety days after Atlantis lost contact with Earth, things were looking quite good.

“Crop yields are increasing dramatically,” Lorne said over a late breakfast. “The botany department is hesitant to plant everything all at once, but the technology and samples from the Nemora have made a huge difference.”

“Excellent,” Sheppard said. “Any ideas on the meat situation?”

“Well, we can’t exactly have slaughter animals running around the city. Dr. Romero suggests we do some hunting on uninhabited worlds, though he has some concerns about upsetting ecosystems. Do we know how the Ancients did it?”

“There’s some speculation that they were vegetarian, which makes sense. Nothing in the database says they didn’t eat meat, but if they did, we don’t know how. I’m not sure we can survive long-term without it.” Humans, while nearly identical to the Ancients, did have some physiological differences, and had evolved to be reliant on animal protein.

“I’m not sure it will be a problem,” Lorne said. “I’m having Beckett work with a nutritionist to double check, but does appear that most of the Nemoran plants were genetically engineered to provide suitable nutrients.”

“That’s excellent, though I’m not sure everyone will be happy with a meatless lifestyle.”

“We’ve adjusted thusfar.”

“Yes we have. Anything else?”

"Last thing: Sgt. Watts has announced that she and Dr. Monroe are expecting a child."

Sheppard's eyes widened in surprise. "Really?" Lorne nodded. "That's excellent."

"Hopefully it's the first of many. Anything else on your end?"

Sheppard glanced over at his notes. “How goes the setup of the Alpha site?”

“All finished. Our computers have been fully networked. I’ve already outlined a rotating skeleton crew so it’s never unmanned, but no one is stuck out there more than once a week.”

“Have I told you that you’re the best military commander I’ve ever worked with?”

Lorne grinned. “As are you, sir.”

“Now, there is the situation with the ZPMs,” Sheppard said.

“Sir?”

“We have five now, near full capacity. I could send three of them back to the colonies, but that would leave us with one on Atlantis, and one on Nemora… if something goes wrong, we would have power to defend ourselves, but not much more. Certainly not enough to move the city again, if necessary.” Some part of him knew it was his own selfishness, that he didn’t want them to be able to call up or send people whenever they wanted. He was not sure he could trust the World Leaders with it. “But we only have a little over a thousand people now, we’re the smallest colony. Is it selfish to keep them?”

“Sir, do you know what day it is?” Lorne asked. Sheppard raised a brow, unsure what he was getting at. “The two month window closed yesterday. You are under no obligation to help any of the colonies, and they’re under no obligation to help us.” He was thoughtful for a moment. “And if, perhaps, you wanted to only provide help to one of them, that’s your decision. The others might not like it, but they couldn’t do anything about it.”

“You’re a very smart man, Colonel.”

“Thank you sir.”

 

Ninety nine days after the fall of Earth, things were coming back together.

 “I’ve cleared another residential area,” Rodney said, putting his toothbrush back in its holder. Next to it, sat Sheppard’s blue one, though he honestly wasn’t sure when it had appeared. “Several people prefer their rooms in the main tower, but a lot are deciding to move outward. The rooms are bigger.”

John could almost hear a question at the end of it, but if it was there, Rodney wasn’t going to voice it. But he understood. Neither of them was the best at this, both had many broken relationships. The future was a scary place, but John knew he’d run long before this point in a lot of his previous relationships, but never considered turning around in this one.

“Bigger rooms, you say?” he asked, kissing Rodney’s shoulders from behind.

“Mmhmm. Jeannie is excited because some of them have kitchens.”

“I like to cook sometimes. I may have forgotten how since moving to Atlantis,” he said slowly, turning Rodney to face him. He’d done his share of rotations in the kitchens in their early days, but most of that had been filling pans with alien produce and reheating military rations.

“Oh?”

John nodded and kissed his neck. “I used to be really good at lasagna. Could probably do something with that meat-substitute Parrish found. You like that stuff, right?”

“I don’t know how they engineered a plant to taste like bacon, but damn is it good.” John bit at one of his nipples; he suppressed a moan.

“Yeah, I could do something with that. Do you like pizza?” he asked.

“Do I like pizza, of course I like pizza.” Who didn’t like pizza?

“I could do that too, I think,” he said, his eyebrows quirked. “And eggs and biscuits and bacon-plant for breakfast. That sounds good, doesn’t it?”

Rodney moaned. “You’re really going to make me say it, aren’t you?”

John grinned and nodded, then kissed his chest.

“Fine. Would you like to move out near the south pier with me?”

“Hmm. I’ll have to think about it,” he said, then kissed the annoyed wrinkle between Rodney’s eyebrows. “I’ve thought about it.”

“Aaand?”

John smirked. It was far too easy to get under Rodney’s skin. “I suppose it wouldn’t be awful.”

“I snore.”

John rolled his eyes. “I know.”

“And I have insomnia.”

“I know that too.” They both had sleep troubles, and often spent the night playing chess or working through math problems. “I can be crabby in the mornings,” he said, pulling Rodney’s shirt over his head.

“Only to be rivaled by my own crabbiness.”

“And sometimes I’m a workaholic. I don’t know how to leave it in the office.”

“Have you ever realized that your flaws and mine are remarkably similar?”

“Think we can handle living together?” John asked, dragging him closer to the bed.

“Your toothbrush says yes.”

“You’ve been conspiring with my toothbrush?”

“Would you just answer the damn question?”

John grinned at him, pecking him on the lips. “Yes, Rodney, we can move out to the pier together.”

“Good.”

“Good,” John repeated, pulling him into the bed.

 

“I love you,” Rodney whispered into his neck as they drifted off to sleep.

“Love you, too,” John said, smiling into his pillow.


End file.
